Research Publications & Scholarly Materials

Research Publications & Scholarly Materials

This is a collection of research conducted with the assistance of the High Performance Computing Cluster. A link to an online version of the articles is provided when available.

Important Notes

  • If you use HPC resources in your research work, we ask that you acknowledge the use of the HPC system in your publications and presentations as "This work made use of the High Performance Computing Resource in the Core Facility for Advanced Research Computing at Case Western Reserve University."
  • Please email references of your published research papers or poster presentations at   to include it here.

Publication Year


  1. H. Zaid, M. H. Berger, D. Jalabert, M. Walls, R. Akrobetu, I. Fongkaew, W. R. L. Lambrecht, N. J. Goble, X. P. A. Gao, P. Berger & A. Sehirlioglu, Atomic-resolved depth profile of strain and cation intermixing around LaAlO3/SrTiO3 interfaces, Scientific Reports 6, Article number: 28118 (2016), doi:10.1038/srep28118
  2. Meng Zhao and Alfred B. Anderson, Predicting pH Dependencies of Electrode Surface Reactions in Electrocatalysis, Electrochemistry Communications 69, 64-67 (2016).

  3. John T. Giblin, Jr., James B. Mertens, and Glenn D. Starkman, Departures from the Friedmann-Lemaitre-Robertston-Walker Cosmological Model in an Inhomogeneous Universe: A Numerical Examination, Phys. Rev. Lett. 116, 251301 – Published 24 June 2016
  4. James B. Mertens, John T. Giblin, Jr., and Glenn D. Starkman, Integration of inhomogeneous cosmological spacetimes in the BSSN formalism, Phys. Rev. D 93, 124059 – Published 24 June 2016
  5. Zhao, X., Liao, Y.-T. T., Johnston, M.C., T’ien, J.S., Ferkul, P.V. and Olson, S.L., Concurrent flame growth, spread and quenching over composite fabric samples in low speed purely forced flow in microgravity, to be presented at the Thirty-Six International Symposium on Combustion, July 31-August 5, 2016, Seoul, Korea
  6.  Mark Hagemann, Churna Bhandari, Walter R. L. Lambrecht, Vibrational modes in the Pmc2_1 structure of ZnGeN_2, Solid State Communications 233 (2016)46–49
  7. In vitro direct and in vivo indirect evidence for the existence of water monomers and the need of chaotic modeling to understand their role in life processes. 9th Chaos Modeling and Simulation International Conference, May 23-26, 2016.
  8. Endo, M. (2016). Numerical modeling of flame spread over spherical solid fuel under low speed flow in microgravity: Model development and comparison to space flight experiments. (Electronic Thesis or Dissertation). Retrieved from
  9. Pathway analysis by randomization incorporating structure-PARIS: an update. Butkiewicz M, Cooke Bailey JN, Frase A, Dudek S, Yaspan BL, Ritchie MD, Pendergrass SA, Haines JL. Bioinformatics. 2016 Mar 7. pii: btw130. [Epub ahead of print] PMID: 27153576
  10. Genetic Association Analysis of Drusen Progression. Hoffman JD, van Grinsven MJ, Li C, Brantley M Jr, McGrath J, Agarwal A, Scott WK, Schwartz SG, Kovach J, Pericak-Vance M, Sanchez CI, Haines JL. Invest Ophthalmol Vis Sci. 2016 Apr 1;57(4):2225-31. doi: 10.1167/iovs.15-18571. PMID: 27116550
  11. The Application of Genetic Risk Scores in Age-Related Macular Degeneration: A Review. Cooke Bailey JN, Hoffman JD, Sardell RJ, Scott WK, Pericak-Vance MA, Haines JL. J Clin Med. 2016 Mar 4;5(3). pii: E31. doi: 10.3390/jcm5030031. Review. PMID: 26959068 Free PMC Article 
  12. Genome-wide association analysis identifies TXNRD2, ATXN2 and FOXC1 as susceptibility loci for primary open-angle glaucoma. Bailey JN, Loomis SJ, Kang JH, Allingham RR, Gharahkhani P, Khor CC, Burdon KP, Aschard H, Chasman DI, Igo RP Jr, Hysi PG, Glastonbury CA, Ashley-Koch A, Brilliant M, Brown AA, Budenz DL, Buil A, Cheng CY, Choi H, Christen WG, Curhan G, De Vivo I, Fingert JH, Foster PJ, Fuchs C, Gaasterland D, Gaasterland T, Hewitt AW, Hu F, Hunter DJ, Khawaja AP, Lee RK, Li Z, Lichter PR, Mackey DA, McGuffin P, Mitchell P, Moroi SE, Perera SA, Pepper KW, Qi Q, Realini T, Richards JE, Ridker PM, Rimm E, Ritch R, Ritchie M, Schuman JS, Scott WK, Singh K, Sit AJ, Song YE, Tamimi RM, Topouzis F, Viswanathan AC, Verma SS, Vollrath D, Wang JJ, Weisschuh N, Wissinger B, Wollstein G, Wong TY, Yaspan BL, Zack DJ, Zhang K, Study EN; ANZRAG Consortium, Weinreb RN, Pericak-Vance MA, Small K, Hammond CJ, Aung T, Liu Y, Vithana EN, MacGregor S, Craig JE, Kraft P, Howell G, Hauser MA, Pasquale LR, Haines JL, Wiggs JL. Nat Genet. 2016 Feb;48(2):189-94. doi: 10.1038/ng.3482. Epub 2016 Jan 11. PMID: 26752265 
  13. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants. Fritsche LG, Igl W, Bailey JN, Grassmann F, Sengupta S, Bragg-Gresham JL, Burdon KP, Hebbring SJ, Wen C, Gorski M, Kim IK, Cho D, Zack D, Souied E, Scholl HP, Bala E, Lee KE, Hunter DJ, Sardell RJ, Mitchell P, Merriam JE, Cipriani V, Hoffman JD, Schick T, Lechanteur YT, Guymer RH, Johnson MP, Jiang Y, Stanton CM, Buitendijk GH, Zhan X, Kwong AM, Boleda A, Brooks M, Gieser L, Ratnapriya R, Branham KE, Foerster JR, Heckenlively JR, Othman MI, Vote BJ, Liang HH, Souzeau E, McAllister IL, Isaacs T, Hall J, Lake S, Mackey DA, Constable IJ, Craig JE, Kitchner TE, Yang Z, Su Z, Luo H, Chen D, Ouyang H, Flagg K, Lin D, Mao G, Ferreyra H, Stark K, von Strachwitz CN, Wolf A, Brandl C, Rudolph G, Olden M, Morrison MA, Morgan DJ, Schu M, Ahn J, Silvestri G, Tsironi EE, Park KH, Farrer LA, Orlin A, Brucker A, Li M, Curcio CA, Mohand-Saïd S, Sahel JA, Audo I, Benchaboune M, Cree AJ, Rennie CA, Goverdhan SV, Grunin M, Hagbi-Levi S, Campochiaro P, Katsanis N, Holz FG, Blond F, Blanché H, Deleuze JF, Igo RP Jr, Truitt B, Peachey NS, Meuer SM, Myers CE, Moore EL, Klein R, Hauser MA, Postel EA, Courtenay MD, Schwartz SG, Kovach JL, Scott WK, Liew G, Tan AG, Gopinath B, Merriam JC, Smith RT, Khan JC, Shahid H, Moore AT, McGrath JA, Laux R, Brantley MA Jr, Agarwal A, Ersoy L, Caramoy A, Langmann T, Saksens NT, de Jong EK, Hoyng CB, Cain MS, Richardson AJ, Martin TM, Blangero J, Weeks DE, Dhillon B, van Duijn CM, Doheny KF, Romm J, Klaver CC, Hayward C, Gorin MB, Klein ML, Baird PN, den Hollander AI, Fauser S, Yates JR, Allikmets R, Wang JJ, Schaumberg DA, Klein BE, Hagstrom SA, Chowers I, Lotery AJ, Léveillard T, Zhang K, Brilliant MH, Hewitt AW, Swaroop A, Chew EY, Pericak-Vance MA, DeAngelis M, Stambolian D, Haines JL, Iyengar SK, Weber BH, Abecasis GR, Heid IM. Nat Genet. 2016 Feb;48(2):134-43. doi: 10.1038/ng.3448. Epub 2015 Dec 21. PMID: 26691988
  14. LICONG CUI, SHIQIANG TAO, GUO-QIANG ZHANG, Biomedical Ontology Quality Assurance Using a Big Data Approach, ACM Transactions on Knowledge Discovery from Data (TKDD), Volume 10 Issue 4, May 2016. [link]
  15. Howell B and McIntyre CC, Analyzing the tradeoff between electrical complexity and accuracy in patient-specific computational models of deep brain stimulation, J Neural Eng. 2016 May 11;13(3):036023.
  16. Murphy BA, Miller JP, Gunalan K, and Ajiboye AB, Contributions of Subsurface Cortical Modulations to Discrimination of Executed and Imagined Grasp Forces through Stereoelectroencephalography, PLoS One. 2016 Mar 10;11(3):e0150359. doi: 10.1371/journal.pone.0150359. eCollection 2016.
  17. Brister, M. M.; Pollum, M.; Crespo-Hernández, C. E. "Photochemical Etiology of Promising Ancestors of the RNA Nucleobases", Phys. Chem. Chem. Phys. 2016, DOI: 10.1039/C6CP00639F. Invited Manuscript; submitted as part of the themed issue on the "Prebiotic Chemistry and the Molecular Origins of Life". 
  18. M. M. Brister; C. E. Crespo-Hernández, “Photochemistry of Promising Ancestral Nucleobases” ACS Meeting-in Miniature, Case Western Reserve University, Cleveland, Ohio, March 4, 2016.
  19. Tong D, Yang S, Lu L (2016) "Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity,"
    Accepted. Journal of Applied Crystallography 
    Meng Zhao and Alfred B. Anderson, Predicting Reversible Potentials in Acid and Base from Self-Consistent Quantum Theory: H(ads) and OH(ads) Deposition on the Pt(111) Electrode, Phys Chem. Lett. 7, 711-714 (2016).
  20. Song L, Ravikumar KM, Huang W, Meng. J, Lu L, and Yang S (2016)" SAXS-driven computational modeling of biomolecular complexes," The Wiley Press (Invited and in press)
  21. Kuynh KW, Cohen MR, Jiang J, Samanta A, Lodowski DT, Zhou ZH, Moiseenkova-Bell VY, Structure of the full-length TRPV2 channel by cryo-EM, Nat Commun. 2016 Mar 29;7:11130. doi: 10.1038/ncomms11130
  22. Stetson LC, Dazard JE, Barnholtz-Sloan JS. Protein markers predict survival in glioma patients. Mol Cell Proteomics. 2016 May 3. pii: mcp.M116.060657. [Epub ahead of print] PubMed PMID: 27143410.
  23. Sun X, Elston RC, Barnholtz-Sloan JS, Falk GW, Grady WM, Faulx A, Mittal SK, Canto M, Shaheen NJ, Wang JS, Iyer PG, Abrams JA, Tian YD, Willis JE, Guda K, Markowitz SD, Chandar A, Warfe JM, Brock W, Chak A. Predicting Barrett's esophagus in Families: An Esophagus Translational Research Network (BETRNet) Model Fitting Clinical Data to a Familial Paradigm. Cancer Epidemiol Biomarkers
    Prev. 2016 Feb 29. pii: cebp.0832.2015. [Epub ahead of print] PubMed PMID: 26929243.
  24. Diaz D.A., Dazard J-E., Rao J.S. Unsupervised Bump Hunting Using Principal Components. In: Ahmed SE, editor. Big and Complex Data Analysis: Methodologies and Applications. Contributions to Statistics, vol.Edited Refereed Volume. Cham Heidelberg New York: Springer (2016 in press). PMCID: pending. 
  25. Dazard J-E., Choe M., LeBlanc M., Rao J.S. Cross-validation and Peeling Strategies for Survival Bump Hunting using Recursive Peeling Methods. Statistical Analysis and Data Mining (2016) 9(1):12-42. PMCID: PMC4809437.
  26. Mark Hagemann, Churna Bhandari,  and Walter R.L. Lambrecht, Vibrational modes in the Pmc21 structure of ZnGeN2, Solid State Communications, Volume 233, May 2016, Pages 46–49.
  27. Mehta BB, Ma D, Griswold MA: Image Registration and Robust Fitting for Motion Insensitive Magnetic Resonance FingerprintingInternational Society of Magnetic Resonance in Medicine 24th Scientific Meeting, Singapore, 2016.
  28. Mehta BB, Ma D, Griswold MA: Reconstruction algorithm for Motion Insensitive Magnetic Resonance Fingerprinting (MRF)International Society of Magnetic Resonance in Medicine Workshop on Data Sampling and Image Reconstruction,Sedona, AZ, USA, 2016. 
  29.  Sparks, R, Madabhushi, A, “Out-of-Sample Extrapolation utilizing Semi-Supervised Manifold Learning (OSE-SSL): Content Based Image Retrieval for Histopathology Images”, Nature Scientific Reports, In Press. 
  30. Janowczyk, A, Basavanhally, A, Madabhushi, A, “Stain Normalization using Sparse AutoEncoders (StaNoSA): Application to digital pathology”, Computerized Medical Imaging and Graphics, In Press. 
  31. Janowczyk, A, Madabhushi, A, “Deep learning for digital pathology image analysis: A comprehensive tutorial with selected use cases”, Journal of Pathology Informatics, In Press. 
  32. Toth, R, Sperling, D, Madabhushi, A, “Quantifying Post- Laser Ablation Prostate Therapy Changes on MRI via a Domain-Specific Biomechanical Model: Preliminary Findings”, PLOS One, In Press.
  33.  Antunes, J, Viswanath, S, Rusu, M, Valls, L, Hoimes, C, Avril, N, Madabhushi, A, “Radiomics analysis on FLT-PET/MRI for characterization of early treatment response in renal cell carcinoma: a proof-of-concept study”, Translational Oncology, 2016 Apr;9(2):155-62. doi: 10.1016/j.tranon.2016.01.008. (PMID:27084432)
  34.  Xu, J, Luo, X, Wang, G, Gilmore, H, Madabhushi, A,”A Deep Convolutional Neural Network for Segmenting and Classifying Epithelial and Stromal Regions in Histopathological Images”, Neurocomputing, vol. 191, pp. 214-223. 
  35. Janowczyk, A, Doyle, S, Gilmore, H, Madabhushi, A, “A resolution adaptive deep hierarchical (RADHicaL) learning scheme applied to nuclear segmentation of digital pathology images”, Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, In Press. 
  36. Bhargava, R and Madabhushi, A, “Emerging Themes in Image Informatics and Molecular Analysis for Digital Pathology”, Annual Reviews of Biomedical Engineering 2016, In Press. 
  37. Wan, T, Bloch, BN, Plecha, D, Thompson, CL, Gilmore, H, Jaffe, C, Harris, L, and Madabhushi, A, "A Radio-genomics Approach for Identifying High Risk Estrogen Receptor-positive Breast Cancers on DCE-MRI: Preliminary Results in Predicting Oncotype DX Risk Scores", Nature Scientific Reports, 2016 Feb 18;6:21394. doi: 10.1038/srep21394 (PMID:26887643) 
  38. Mark Turner, “Cyberinfrastructure for the study of multimodal communication—language, gesture, art.” Cyberinfrastructure Conference. Case Western Reserve University. 11 May 2016.
  39. Mark Turner, “Hands-on tutorial on new tools from the Distributed Little Red Hen Lab.” International Workshop on Multimodal Construction Grammar. University of Osnabrück, 11 March 2016. 
  40. Mark Turner, “Cyber & statistical tools for the study of speech gesture, iconography, and other systems of visual communication.” International Workshop on Multimodal Construction Grammar. University of Osnabrück, 10 March 2016.
  41. Mark Turner, “New Big Data Tools for Gesture Research.” Free University, Berlin. 4 March 2016.
  42. Mark Turner, “Red Hen Methods for Film Research.” Cinepoetics Institute, Free University, Berlin. 4 March 2016.  INVITED


  1. Liao JY and Kirsch RF. (2015) Velocity neurons improve performance more than goal or position neurons do in a simulated closed-loop BCI arm-reaching task. Front. Comput. Neurosci. 9:84. doi: 10.3389/fncom.2015.00084
  2. Liao JY, Kirsch RF. (2014) Characterizing and Predicting Submovements during Human Three-Dimensional Arm Reaches. PLoS ONE 9(7): e103387. doi:10.1371/journal.pone.0103387
  3.  Numerical Modeling of Upward Flame Spread and Burning of Wavy Thin Solids EJ Stalcup - 2015 -
  4. Brister, M. M.; Crespo-Hernández, C. E. "Direct Observation of Triplet-State Population Dynamics in the RNA Uracil Derivative 1-Cyclohexyluracil", J. Phys. Chem. Lett. 2015, 6, 4404-4409
  5. Estimating cumulative pathway effects on risk for age-related macular degeneration using mixed linear models. Hall JB, Cooke Bailey JN, Hoffman JD, Pericak-Vance MA, Scott WK, Kovach JL, Schwartz SG, Agarwal A, Brantley MA Jr, Haines JL, Bush WS. BMC Bioinformatics. 2015 Oct 14;16:329. doi: 10.1186/s12859-015-0760-4. PMID: 26467978 Free PMC Article 
  6. Rapidly progressive Alzheimer's disease features distinct structures of amyloid-β. Cohen ML, Kim C, Haldiman T, ElHag M, Mehndiratta P, Pichet T, Lissemore F, Shea M, Cohen Y, Chen W, Blevins J, Appleby BS, Surewicz K, Surewicz WK, Sajatovic M, Tatsuoka C, Zhang S, Mayo P, Butkiewicz M, Haines JL, Lerner AJ, Safar JG. Brain. 2015 Apr;138(Pt 4):1009-22. doi: 10.1093/brain/awv006. Epub 2015 Feb 15. PMID: 25688081 Free Article 
  7. Examination of candidate exonic variants for association to Alzheimer disease in the Amish. D'Aoust LN, Cummings AC, Laux R, Fuzzell D, Caywood L, Reinhart-Mercer L, Scott WK, ericak-Vance MA, Haines JL. PLoS One. 2015 Feb 10;10(2):e0118043. doi: 10.1371/journal.pone.0118043. eCollection 2015. PMID: 25668194 Free PMC Article
  8. Meta-analysis of Genome-Wide Association Studies Identifies Novel Loci Associated With Optic Disc Morphology. Springelkamp H, Mishra A, Hysi PG, Gharahkhani P, Höhn R, Khor CC, Cooke Bailey JN, Luo X, Ramdas WD, Vithana E, Koh V, Yazar S, Xu L, Forward H, Kearns LS, Amin N, Iglesias AI, Sim KS, van Leeuwen EM, Demirkan A, van der Lee S, Loon SC, Rivadeneira F, Nag A, Sanfilippo PG, Schillert A, de Jong PT, Oostra BA, Uitterlinden AG, Hofman A; NEIGHBORHOOD Consortium, Zhou T, Burdon KP, Spector TD, Lackner KJ, Saw SM, Vingerling JR, Teo YY, Pasquale LR, Wolfs RC, Lemij HG, Tai ES, Jonas JB, Cheng CY, Aung T, Jansonius NM, Klaver CC, Craig JE, Young TL, Haines JL, MacGregor S, Mackey DA, Pfeiffer N, Wong TY, Wiggs JL, Hewitt AW, van Duijn CM, Hammond CJ. Genet Epidemiol. 2015 Mar;39(3):207-16. doi: 10.1002/gepi.21886. Epub 2015 Jan 28. PMID: 25631615 Free PMC Article
  9. Tang S, Fox TL, Lo T-Y, Horton JM, Ho R-M, Zhao B, Stewart PL, Zhu L. Environmentally responsive self-assembly of mixed poly(tert-butyl acrylate)/polystyrene brush-grafted silica nanoparticles in selective polymer matrices. (2015) Soft Matter, 11:5501-5512
  10. Fox TL, Tang S, Horton JM, Holdaway HA, Zhao B, Zhu L, Stewart PL. In-situ characterization of binary mixed polymer brush-grafted silica nanoparticles in aqueous and organic solvents by cryo-electron tomography. (2015) Langmuir, 31:8680-8688.
  11.  M. M. Brister; C. E. Crespo-Hernández, “Ultrafast Dynamics in DNA and RNA Derivatives Monitored by Broadband Transient Absorption Spectroscopy”, 70th International Symposium on Molecular Spectroscopy, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, June 22 to 26, 2015.
  12. M. M. Brister; C. E. Crespo-Hernández, “Excited-State Dynamics in the RNA Base Analogue 1-Cyclohexyluracil in Acetonitrile”, 6th Ohio Photochemical Society Meeting, Oregon, Ohio, May 27 to 29, 2015.
  13. M   M. M. Brister; C. E. Crespo-Hernández, “Nucleic Acid Derivatives’ Ultrafast Dynamics utilizing Broadband Transient Absorption Spectroscopy”, Chemistry Graduate Student Symposium, University at Buffalo, The State University of New York, Buffalo, New York, May 18 to 20, 2015.
  14. Huang W, Ravikumar KM, Chance MR, and Yang S (2015) “Quantitative mapping of protein structure by hydroxyl radical footprinting mediated structural mass spectrometry: A protection factor analysis," Biophys. J. 108 (1) 107–115
  15. Kaur P, Kiselar J, Yang S, and Chance MR (2015) “Quantitative protein topography analysis and high-resolution structure prediction using hydroxyl radical labeling and tandem-ion mass spectrometry", Molecular and Cellular Proteomics, 14 (4) 1159–1168 [Application of the protection factor analysis for single-residue footprinting data] Voss-Hoynes HA, Stein C, Truitt B, Tag J, et al. Genome wide association in families identifies a genetic basis for two components of speech, phonological processing and articulation, (1069). Presented at the 65 th Annual Meeting of the American Society of Human Genetics, October 9, 2015.
  16. Yu M, O'Leary RM, Kaz AM, Morris SM, Carter KT, Chak A, Chandar A, Willis JE, Moinova HR, Markowitz SD, Brenner DE, Anandabapasathy S, Westerhoff M, Wong CJ, Shaheen NJ, Chen Y, Barnholtz-Sloan JS, Grady WM. Methylated B3GAT2 and ZNF793
  17. Are Potential Detection Biomarkers for Barrett's Esophagus. Cancer Epidemiol Biomarkers Prev. 2015 Dec;24(12):1890-7. doi: 10.1158/1055-9965.EPI-15-0370. Epub 2015 Nov 6. PubMed PMID: 26545406; PubMed Central PMCID: PMC4670566.
  18. Varadan V, Singh S, Nosrati A, Ravi L, Lutterbaugh J, Barnholtz-Sloan JS, Markowitz SD, Willis JE, Guda K. ENVE: a novel computational framework characterizes copy-number mutational landscapes in colorectal cancers from African American patients. Genome Med. 2015 Jul 20;7(1):69. doi: 10.1186/s13073-015-0192-9. eCollection 2015. PubMed PMID: 26269717; PubMed Central PMCID: PMC4534088.
  19. Virk SM, Gibson RM, Quinones-Mateu ME, Barnholtz-Sloan JS. Identification of variants in primary and recurrent glioblastoma using a cancer-specific gene panel and whole exome sequencing. PLoS One. 2015 May 7;10(5):e0124178. doi: 10.1371/journal.pone.0124178. eCollection 2015. PubMed PMID: 25950952; PubMed Central PMCID: PMC4423782.
  20. Stetson LC, Pearl T, Chen Y, Barnholtz-Sloan JS. Computational identification of multi-omic correlates of anticancer therapeutic response. BMC Genomics. 2014;15 Suppl 7:S2. doi: 10.1186/1471-2164-15-S7-S2. Epub 2014 Oct 27. Erratum in: BMC Genomics. 2015;16:481. PubMed PMID: 25573145; PubMed Central PMCID: PMC4243102.
  21. Ochs-Balcom HM, Sun X, Chen Y, Barnholtz-Sloan J, Erwin DO, Jandorf L, Sucheston-Campbell L, Elston RC. Putative linkage signals identified for breast cancer in African American families. Cancer Epidemiol Biomarkers Prev. 2015 Feb;24(2):442-7. doi: 10.1158/1055-9965.EPI-14-1131. Epub 2014 Dec 4. PubMed PMID: 25477366; PubMed Central PMCID: PMC4323921.
  22. Clingingsmith, D. (2015), Are The World's Languages Consolidating? The Dynamics and Distribution of Language Populations. The Economic Journal. doi: 10.1111/ecoj.12257
  23. Jagodnik, K.M., Blana, D., van den Bogert, A.J. and Kirsch, R.F., 2015. An optimized proportional-derivative controller for the human upper extremity with gravity. Journal of Biomechanics48(13), pp.3692-3700.
  24. Jiankui Yuan, Yiran Zheng, Barry Wessels, Simon S. Lo, Rodney Ellis, Mitchell Machtay,and Min Yao, Experimental Validation of Monte Carlo Simulations Based on a Virtual Source Model for TomoTherapy in a RANDO Phantom, Technology in Cancer Research & Treatment 1–9, 2015.
  25. Chris Fietkiewicz and Christopher G. Wilson, Variability in respiratory rhythm generation: in vitro and in silico models, Communications in Nonlininear Science and Numerical Simulation, August 2015 [paper]
  26. Churna Bhandari and Walter R. L. Lambrecht, Electronic and magnetic properties of electron-doped V2O5and NaV2O5, Phys. Rev. B 92, 125133 – Published 17 September 2015 [paper]
  27. Sanjaya Gajurel and Roger Bielefeld, Mutated Near Optimal Vertex Cover Algorithm (NOVCA) Visualization on a Tile Display, IEEE Cluster 2015, Sep. 8-11 [poster] [paper]
  28. Sanjaya Gajurel and Roger Bielefeld, Mutated Vertex Cover Algorithm Implemented at CWRU High
    Performance Computing Cluster, ShowCase April 2015 [poster]
  29. Churna Bhandari, Walter R. L. Lambrecht, and Mark van Schilfgaarde,Quasiparticle self-consistent GW calculations of the electronic band structure of bulk and monolayer V2O5, Phys. Rev. B 91, 125116
  30. Jiankui Yuan, Yi Rong , Quan Chen, A virtual source model for Monte Carlo simulation of helical TomoTherapy, Journal of Applied Clinical Medial Physics, Vol 16, No.1 (2015) 69-85, link
  31. Fully opposite spin polarization of electron and hole bands in DyN and related band structures of GdN and HoN Tawinan Cheiwchanchamnangij and Walter R. L. Lambrecht, Phys. Rev. B 92, 035134 (2015) - Published 20 July 2015.
  32. Charge-neutral disorder and polytypes in heterovalent wurtzite-based ternary semiconductors: The importance of the octet rule , Paul C. Quayle, Eric W. Blanton, Atchara Punya, Grant T. Junno, Keliang He, Lu Han, Hongping Zhao, Jie Shan, Walter R. L. Lambrecht, and Kathleen Kash, Phys. Rev. B 91, 205207 (2015) - Published 18 May 2015
  33. First-principles calculations of phonons and Raman spectra in monoclinic CsSnCl3, Ling-yi Huang and Walter R. L. Lambrecht, Phys. Rev. B 91, 075206 (2015) - Published 20 February 2015. 
  34. Tiwari, P, Danish, S, Jiang, B, Madabhushi, A, “Association of computerized texture features on MRI with early treatment response following laser ablation for neuropathic cancer pain: preliminary findings”, J Med Imaging. 2015 Oct;2(4):041008. doi: 10.1117/1.JMI.2.4.041008. Epub 2015 Sep 25. (PMID: 26870745). 
  35. Varadan, V, Kamalakaran, S, Gilmore, H, Banerjee, N, Janevski, A, Miskimen, K, Williams, N, Basavanhally, A, Madabhushi, A, Lezon-Geyda, K, Bossuyt, V, Lannin, D, Abu-Khalaf, M, Sikov, W, Dimitrova, N, Harris, L, “Brief-exposure to preoperative bevacizumab reveals a TGF-β signature predictive of response in HER2-negative breast cancers”, Int J Cancer. 2015 Aug 18. doi: 10.1002/ijc.29808. [Epub ahead of print] (PMID: 26284485). 
  36.  Xu, J, Xiang, L, Liu, Q, Gilmore, H, Wu, J, Tang, J, Madabhushi, A, “Stacked Sparse Autoencoder (SSAE) for Nuclei Detection on Breast Cancer Histopathology images”, IEEE Transactions on Medical Imaging, 2015 Jul 20. [Epub ahead of print] (PMID: 26208307).
  37.   Rusu, M, Wang, H, Golden, Thea, Gow, A, Madabhushi, A, “Framework for 3D histologic reconstruction and fusion with in vivo MRI: Preliminary results of characterizing pulmonary inflammation in a mouse model”, Medical Physics, 42(8):4822. doi: 10.1118/1.4923161., (PMID: 26233209). 
  38. Ginsburg, S, Lee, G, Ali, S, Madabhushi, A, Feature Importance in Nonlinear Embeddings (FINE): Applications in Digital Pathology, IEEE Transactions on Medical Imaging, 2015 Jul 14. [Epub ahead of print] PMID: 26186772). 
  39. Litjens, G, Huisman, H, Elliot, R, Shih, N, Feldman, M, Viswanath, S, Bomers, J, Madabhushi, A, “Computer-extracted features can distinguish benign confounding disease from prostatic adenocarcinoma on multi-parametric MRI”, Radiology, 2015 Jul 17:142856. [Epub ahead of print] (PMID: 26192734). 
  40. Shridar, A, Doyle, S, Madabhushi, A, “Content-Based Image Retrieval of Digitized Histopathology in Boosted Spectrally Embedded Spaces”, Journal of Pathology Informatics, Jun 29;6:41. doi: 10.4103/2153-3539.159441. eCollection 2015 (PMID: 26167385)
  41. Singanamalli, A, Sparks, R, Rusu, M, Shih, N, Ziober, A, Tomaszewski, J, Rosen, M, Feldman, M, Madabhushi, A, “Identifying in vivo DCE MRI markers associated with Microvessel Architecture and Gleason Grades of Prostate Cancer—Preliminary Findings”, Journal of Magnetic Resonance Imaging, doi: 10.1002/jmri.24975. [Epub ahead of print] (PMID:26110513)
  42. Basavanhally, A, Viswanath, S, Madabhushi, A, “Predicting Classifier Performance with Limited Training Data: Applications to Computer-Aided Diagnosis in Breast and Prostate Cancer”, PLOS One, 2015 May 18;10(5):e0117900. doi: 10.1371/journal.pone.0117900. eCollection 2015. (PMID:25993029)
  43. Xu, J, Xiang, L, Wang, G, Ganesan, S, Feldman, M, Shih, N, Gilmore, H, Madabhushi, A, “Sparse Non-negative Matrix Factorization (SNMF) based Color Unmixing for Breast Histopathological Image Analysis”, Computerized Medical Imaging and Graphics (CMIG), pii: S0895-6111(15)00077-4. doi: 10.1016/j.compmedimag.2015.04.002. [Epub ahead of print] (PMID: 25958195).
  44. Ittipon Fongkaew, Sukit Limpijumnong, and Walter R. L. Lambrecht, Effects of structural relaxation, interdiffusion, and surface termination on two-dimensional electron gas formation at the LaAlO3/SrTiO3 (001) interface, Phys. Rev. B 92, 155416 – Published 12 October 2015.
  45. Alfred B. Anderson and Meng ZhaoReaction Energy for an Electrode Surface Atom Inserting into an R-H Bond and its Dependence on Electrode Potential: Application to Pt(111), J. Electrochem. Soc., 162, H583-H589 (2015).
  46. A. Asiri and A. B. Anderson, Mechanisms for Ethanol Electrooxidation on Pt(111) and Adsorption Bond Strengths Defining the Ideal Catalyst, J. Electrochem. Soc., 162 (1) F115-F122 (2015).
  47.  Dazard J-E., Choe M., LeBlanc M., Rao J.S. R package PRIMsrc: Bump Hunting by Patient Rule Induction Method for Survival, Regression and Classification. In JSM Proceedings, Statistical Programmers and Analysts Section. Seattle, WA, USA. American Statistical Association-IMS (2015) p. 650-664. PMCID: PMC4718587. 
  48. Jiayuan Miao, Ram S. Bhatta, D. H. Reneker, M. Tsige, and P. L. Taylor, “Molecular dynamics simulations of relaxation in stretched PVDF nanofibers”, Polymer 56 482  (2015). 
  49. Mark Turner, “Big Data Science for Multimodal Construction Grammar: A Research Program for the Digital Humanities and Social Sciences.” Awards Ceremony of the Anneliese Maier Research Prize from the Alexander von Humboldt Foundation. Leipzig. 15 September 2015. 
  50. Mark Turner, “Recent Results from the Red Hen Lab.” Conference on Empirical Methods in Cognitive Linguistics, 7. João Pessoa, Brazil, 8 August 2015.
  51. Mark Turner, “Studying Political Communication in a Massive Dataset: Recent Results from the Red Hen Lab.” Duke-Oxford Conference on Cognitive Approaches to Law, Economics, Politics and Policy. Duke University. 5 June 2015.
  52. Mark Turner, “Big Data Science for the Arts and Humanities: How to study 3 billion words and 250,000 hours of human communication.” Conference on Culture and Professions of the Future: Humanities as the Arts and Technology. University of Łódź, Poland. 4 May 2015. 


  1. John T. Giblin, Jr. and James B. Mertens, Gravitational radiation from first-order phase transitions in the presence of a fluid, Phys. Rev. D 90, 023532 – Published 22 July 2014

  2. Villarreal SA, Stewart PL. CryoEM and image sorting for flexible protein/DNA complexes. (2014) J. Struct. Biol., 187:76-83.

  3. Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process. Springelkamp H, Höhn R, Mishra A, Hysi PG, Khor CC, Loomis SJ, Bailey JN, Gibson J, Thorleifsson G, Janssen SF, Luo X, Ramdas WD, Vithana E, Nongpiur ME, Montgomery GW, Xu L, Mountain JE, Gharahkhani P, Lu Y, Amin N, Karssen LC, Sim KS, van Leeuwen EM, Iglesias AI, Verhoeven VJ, Hauser MA, Loon SC, Despriet DD, Nag A, Venturini C, Sanfilippo PG, Schillert A, Kang JH, Landers J, Jonasson F, Cree AJ, van Koolwijk LM, Rivadeneira F, Souzeau E, Jonsson V, Menon G; Blue Mountains Eye Study—GWAS group, Weinreb RN, de Jong PT, Oostra BA, Uitterlinden AG, Hofman A, Ennis S, Thorsteinsdottir U, Burdon KP; NEIGHBORHOOD Consortium; Wellcome Trust Case Control Consortium 2 (WTCCC2), Spector TD, Mirshahi A, Saw SM, Vingerling JR, Teo YY, Haines JL, Wolfs RC, Lemij HG, Tai ES, Jansonius NM, Jonas JB, Cheng CY, Aung T, Viswanathan AC, Klaver CC, Craig JE, Macgregor S, Mackey DA, Lotery AJ, Stefansson K, Bergen AA, Young TL, Wiggs JL, Pfeiffer N, Wong TY, Pasquale LR, Hewitt AW, van Duijn CM, Hammond CJ. Nat Commun. 2014 Sep 22;5:4883. doi: 10.1038/ncomms5883. PMID: 25241763 Free PMC Article

  4. Genome-wide association studies: getting to pathogenesis, the role of inflammation/complement in age-related macular degeneration. Cooke Bailey JN, Pericak-Vance MA, Haines JL. Cold Spring Harb Perspect Med. 2014 Sep 11;4(12):a017186. doi: 10.1101/cshperspect.a017186. Review. PMID: 25213188

  5. Effects of multiple genetic loci on age at onset in late-onset Alzheimer disease: a genome-wide association study. Naj AC, Jun G, Reitz C, Kunkle BW, Perry W, Park YS, Beecham GW, Rajbhandary RA, Hamilton-Nelson KL, Wang LS, Kauwe JS, Huentelman MJ, Myers AJ, Bird TD, Boeve BF, Baldwin CT, Jarvik GP, Crane PK, Rogaeva E, Barmada MM, Demirci FY, Cruchaga C, Kramer PL, Ertekin-Taner N, Hardy J, Graff-Radford NR, Green RC, Larson EB, St George-Hyslop PH, Buxbaum JD, Evans DA, Schneider JA, Lunetta KL, Kamboh MI, Saykin AJ, Reiman EM, De Jager PL, Bennett DA, Morris JC, Montine TJ, Goate AM, Blacker D, Tsuang DW, Hakonarson H, Kukull WA, Foroud TM, Martin ER, Haines JL, Mayeux RP, Farrer LA, Schellenberg GD, Pericak-Vance MA; Alzheimer Disease Genetics Consortium, Albert MS, Albin RL, Apostolova LG, Arnold SE, Barber R, Barnes LL, Beach TG, Becker JT, Beekly D, Bigio EH, Bowen JD, Boxer A, Burke JR, Cairns NJ, Cantwell LB, Cao C, Carlson CS, Carney RM, Carrasquillo MM, Carroll SL, Chui HC, Clark DG, Corneveaux J, Cribbs DH, Crocco EA, DeCarli C, DeKosky ST, Dick M, Dickson DW, Duara R, Faber KM, Fallon KB, Farlow MR, Ferris S, Frosch MP, Galasko DR, Ganguli M, Gearing M, Geschwind DH, Ghetti B, Gilbert JR, Glass JD, Growdon JH, Hamilton RL, Harrell LE, Head E, Honig LS, Hulette CM, Hyman BT, Jicha GA, Jin LW, Karydas A, Kaye JA, Kim R, Koo EH, Kowall NW, Kramer JH, LaFerla FM, Lah JJ, Leverenz JB, Levey AI, Li G, Lieberman AP, Lin CF, Lopez OL, Lyketsos CG, Mack WJ, Martiniuk F, Mash DC, Masliah E, McCormick WC, McCurry SM, McDavid AN, McKee AC, Mesulam M, Miller BL, Miller CA, Miller JW, Murrell JR, Olichney JM, Pankratz VS, Parisi JE, Paulson HL, Peskind E, Petersen RC, Pierce A, Poon WW, Potter H, Quinn JF, Raj A, Raskind M, Reisberg B, Ringman JM, Roberson ED, Rosen HJ, Rosenberg RN, Sano M, Schneider LS, Seeley WW, Smith AG, Sonnen JA, Spina S, Stern RA, Tanzi RE, Thornton-Wells TA, Trojanowski JQ, Troncoso JC, Valladares O, Van Deerlin VM, Van Eldik LJ, Vardarajan BN, Vinters HV, Vonsattel JP, Weintraub S, Welsh-Bohmer KA, Williamson J, Wishnek S, Woltjer RL, Wright CB, Younkin SG, Yu CE, Yu L. JAMA Neurol. 2014 Nov;71(11):1394-404. doi: 10.1001/jamaneurol.2014.1491. Erratum in: JAMA Neurol. 2014 Nov;71(11):1457. PMID: 25199842 Free PMC Article
  6. Genome-wide analysis of multi-ancestry cohorts identifies new loci influencing intraocular pressure and susceptibility to glaucoma. Hysi PG, Cheng CY, Springelkamp H, Macgregor S, Bailey JN, Wojciechowski R, Vitart V, Nag A, Hewitt AW, Höhn R, Venturini C, Mirshahi A, Ramdas WD, Thorleifsson G, Vithana E, Khor CC, Stefansson AB, Liao J, Haines JL, Amin N, Wang YX, Wild PS, Ozel AB, Li JZ, Fleck BW, Zeller T, Staffieri SE, Teo YY, Cuellar-Partida G, Luo X, Allingham RR, Richards JE, Senft A, Karssen LC, Zheng Y, Bellenguez C, Xu L, Iglesias AI, Wilson JF, Kang JH, van Leeuwen EM, Jonsson V, Thorsteinsdottir U, Despriet DD, Ennis S, Moroi SE, Martin NG, Jansonius NM, Yazar S, Tai ES, Amouyel P, Kirwan J, van Koolwijk LM, Hauser MA, Jonasson F, Leo P, Loomis SJ, Fogarty R, Rivadeneira F, Kearns L, Lackner KJ, de Jong PT, Simpson CL, Pennell CE, Oostra BA, Uitterlinden AG, Saw SM, Lotery AJ, Bailey-Wilson JE, Hofman A, Vingerling JR, Maubaret C, Pfeiffer N, Wolfs RC, Lemij HG, Young TL, Pasquale LR, Delcourt C, Spector TD, Klaver CC, Small KS, Burdon KP, Stefansson K, Wong TY; BMES GWAS Group; NEIGHBORHOOD Consortium; Wellcome Trust Case Control Consortium 2, Viswanathan A, Mackey DA, Craig JE, Wiggs JL, van Duijn CM, Hammond CJ, Aung T. Nat Genet. 2014 Oct;46(10):1126-30. doi: 10.1038/ng.3087. Epub 2014 Aug 31. PMID: 25173106 Free PMC Article
  7. Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma. Gharahkhani P, Burdon KP, Fogarty R, Sharma S, Hewitt AW, Martin S, Law MH, Cremin K, ailey JN, Loomis SJ, Pasquale LR, Haines JL, Hauser MA, Viswanathan AC, McGuffin P, Topouzis F, Foster PJ, Graham SL, Casson RJ, Chehade M, White AJ, Zhou T, Souzeau E, Landers J, Fitzgerald JT, Klebe S, Ruddle JB, Goldberg I, Healey PR; Wellcome Trust Case Control Consortium 2; NEIGHBORHOOD Consortium, Mills RA, Wang JJ, Montgomery GW, Martin NG, Radford-Smith G, Whiteman DC, Brown MA, Wiggs JL, Mackey DA, Mitchell P, MacGregor S, Craig JE. Nat Genet. 2014 Oct;46(10):1120-5. doi: 10.1038/ng.3079. Epub 2014 Aug 31. PMID: 25173105 Free PMC Article
  8. Hypothesis-independent pathway analysis implicates GABA and acetyl-CoA metabolism in primary open-angle glaucoma and normal-pressure glaucoma. Bailey JN, Yaspan BL, Pasquale LR, Hauser MA, Kang JH, Loomis SJ, Brilliant M, Budenz DL, Christen WG, Fingert J, Gaasterland D, Gaasterland T, Kraft P, Lee RK, Lichter PR, Liu Y, McCarty CA, Moroi SE, Richards JE, Realini T, Schuman JS, Scott WK, Singh K, Sit AJ, Vollrath D, Wollstein G, Zack DJ, Zhang K, Pericak-Vance MA, Allingham RR, Weinreb RN, Haines JL, Wiggs JL. Hum Genet. 2014 Oct;133(10):1319-30. doi: 10.1007/s00439-014-1468-7. Epub 2014 Jul 19. PMID: 25037249 Free PMC Article
  9. Rare complement factor H variant associated with age-related macular degeneration in the Amish. Hoffman JD, Cooke Bailey JN, D'Aoust L, Cade W, Ayala-Haedo J, Fuzzell D, Laux R, Adams LD, Reinhart-Mercer L, Caywood L, Whitehead-Gay P, Agarwal A, Wang G, Scott WK, Pericak-Vance MA, Haines JL. Invest Ophthalmol Vis Sci. 2014 Jun 6;55(7):4455-60. doi: 10.1167/iovs.13-13684. PMID: 24906858 Free PMC Article
  10. Dazard J-E., Choe M., LeBlanc M., Rao J.S. Cross-Validation of Survival Bump Hunting using Recursive Peeling Methods. In JSM Proceedings, Survival Methods for Risk Estimation/Prediction Section. Boston, MA, USA: American Statistical Association-IMS (2014) p. 3366-3380. PMCID: PMC4795911.

  11. Wildey G, Chen Y, Lent I, Stetson L, Pink J, Barnholtz-Sloan JS, Dowlati A. Pharmacogenomic approach to identify drug sensitivity in small-cell lung cancer. PLoS One. 2014 Sep 8;9(9):e106784. doi: 10.1371/journal.pone.0106784. eCollection 2014. PubMed PMID: 25198282; PubMed Central PMCID: PMC4157793.

  12. Guan X, Vengoechea J, Zheng S, Sloan AE, Chen Y, Brat DJ, O'Neill BP, de Groot J, Yust-Katz S, Yung WK, Cohen ML, Aldape KD, Rosenfeld S, Verhaak RG, Barnholtz-Sloan JS. Molecular subtypes of glioblastoma are relevant to lower grade glioma. PLoS One. 2014 Mar 10;9(3):e91216. doi: 10.1371/journal.pone.0091216. eCollection 2014. PubMed PMID: 24614622; PubMed Central PMCID: PMC3948818.
  13.  Lai RK, Chen Y, Guan X, Nousome D, Sharma C, Canoll P, Bruce J, Sloan AE, Cortes E, Vonsattel JP, Su T, Delgado-Cruzata L, Gurvich I, Santella RM, Ostrom Q, Lee A, Gregersen P, Barnholtz-Sloan J. Genome-wide methylation analyses in glioblastoma multiforme. PLoS One. 2014 Feb 21;9(2):e89376. doi: 10.1371/journal.pone.0089376. eCollection 2014. PubMed PMID: 24586730; PubMed Central PMCID: PMC3931727.
  14. Churna Bhandari and Walter R. L. Lambrecht, Phonons and related spectra in bulk and monolayer V2O5, Phys. Rev. B 89, 045109
  15. Lattice dynamics in perovskite halides CsSnX3 with X=I, Br, Cl, Ling-yi Huang and Walter R. L. Lambrecht, Phys. Rev. B 90, 195201 (2014) - Published 5 November 2014
  16. J. Casey Johnson, LaShanda T. J. Korley, & Mesfin Tsige, Coarse-Grained Modeling of Peptidic/PDMS Triblock Morphology, J. Phys. Chem. B, 2014, 118 (47), pp 13718–13728, DOI: 10.1021/jp506553v [Link]

  17. Gajurel, S. and Bielefeld, R., A Heuristic Approach to Fast NOVCA (Near Optimal Vertex Cover Algorithm), JCTA 5 (2014) 83-90. [Link]

  18. Doi E, Lewicki MS (2014) A Simple Model of Optimal Population Coding for Sensory Systems. PLoS Comput Biol 10(8): e1003761. doi:10.1371/journal.pcbi.1003761 [Link]  

  19. Huynh KW, Cohen MR, Chakrapani S, Holdaway HA, Stewart PL, Moiseenkova-Bell VY. (2014) Structural insight into the assembly of TRPV channels. Structure, 22:260-268.

  20. Gulati N, Smith JG, Nemerow GR, Stewart PL. (2014) CryoEM based models for Adenovirus neutralization by human alpha-defensin 5. Microscopy and Microanalysis.

  21. Irons E, Di Paolo N, Shayakhmetov D, Stewart P. (2014) Blood coagulation factors in disseminated adenovirus infection: How structural differences define biological tropism and immune response. Annual Clinical Virology Symposium, Daytona Beach, FL.

  22. Gulati NM, Villarreal SA, Gulati S, Palczewski K, Stewart PL. (2014). Imaging of Isolated Disk Architecture from Rod Outer Segments of the Retina by Cryo-Electron Tomography. Biomedical Graduate Student Symposium.

  23. Gulati NM, Villarreal SA, Gulati S, Palczewski K, Stewart PL. (2014). Imaging of Isolated Disk Architecture from Rod Outer Segments of the Retina by Cryo-Electron Tomography. Research ShowCase.

  24. Gulati NM, Villarreal SA, Gulati S, Palczewski K, Stewart PL. (2014). Imaging of Isolated Disk Architecture from Rod Outer Segments of the Retina by Cryo-Electron Tomography. Cryo-EM 3D Image Analysis Symposium, Lake Tahoe, CA.

  25. Gulati NM, Villarreal SA, Gulati S, Palczewski K, Stewart PL. (2014). Imaging of Isolated Disk Architecture from Rod Outer Segments of the Retina by Cryo-Electron Tomography. Microscopy Society of Northeastern Ohio Meeting, University Heights, OH.

  26. J. N. Wisotsky, X. Han, and Y. Zhang "Uncovering the Role of lncRNA in response to DNA Damage.", Poster Presentation at Genetics and Genome Sciences Retreat and Biological Graduate Student Symposium, Case Western, 2014

  27. Liqun Zhang, Matthias Buck, “Structure and dynamics of the plexin-B1 transmembrane receptor bound to GTPases “, Biophysical Society, San Francisco, CA, 2014 + Travel awards to attend the Biophysics Society meeting, sponsored by the Education, Minority Affairs, and Professional Opportunities for Women Committees. San Francisco, California, February, 15-19, 2014.

  28. A. B. Anderson and H. A. Asiri, "Reversible Potentials for Steps in Methanol and Formic Acid Oxidation to CO2; Adsorption Energies of Intermediates on the Ideal Electrocatalyst for Methanol Oxidation and CO2 Reduction: Phys. Chem. Chem. Phys. 16 (22), 10587-10599 (2014)

  29. Mahdi Orooji ; Rachel Sparks ; B. Nicolas Bloch ; Ernest Feleppa ; Dean Barratt ; Anant Madabhushi; "Spatially aware expectation maximization (SpAEM): application to prostate TRUS segmentation". Proc. SPIE 9034, Medical Imaging 2014: Image Processing, 90343Y (March 21, 2014); doi:10.1117/12.2043981.

  30. Miao, Jiayuan, Gavin R. Brown, and Philip L. Taylor. "Theoretically guided design of efficient polymer dielectrics." Journal of Applied Physics 115.9 (2014): 094104.

  31. M. Zhao, A. B. Anderson, R. Akolkar, and R. Jinnouchi,"Using Theory to Understand the Autocatalysis of Cu Electroless Deposition ", Poster Presentation at Research ShowCase 2014.

  32. C Fietkiewicz, CG Wilson, “Variability in respiratory rhythm generation: in vitro and in silico models”, Nonlinear dynamics and stochastic methods: from neuroscience to other biological applications, Pittsburgh, PA, March 2014.

  33. Yang, Y.; Campana, C. F.; Cheng, G.; Peng, X.; Kenney, M. E. “The structure and properties of a sheathed, low reactivity silicon phthalocyanine and the potential for still more inert phthalocyanines” J. Porphyrins Phthalocyanines 2014 DOI: 10.1142/S1088424614500060.

  34. Grandhi S and Laframboise T. "High-throughput Analysis of the Human Mitochondrial Regulome in Cancer". First Place Poster Presentation at Research ShowCASE 2014

  35. A Knappenberger, MF Ahmad, C Dealwis, ME Harris. “Translational investigation of ribonucleotide reductase.” 1st Place Winner, Poster Presentation at Research ShowCase 2014. [Link to Poster]

  36. Corradin O, Saiakhova A, Akhtar-Zaidi B, Myeroff L, Willis J, Cowper-Sal lari R, Lupien M, Markowitz S, Scacheri PC. 2014. Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits.Genome research 24(1): 1-13

  37.  Senevirathna, W.; Daddario, C. M.; Sauve, G. “Density functional theory study predicts low reorganization energies for azadipyrromethene-based metal complexes”, J. Phys. Chem. Lett., 2014, 5, 935-941.

  38. Fernando, R.; Mao, Z.; Muller, E.; Ruan, F.; Sauvé, G. “Tuning the organic solar cell performance of acceptor 2,6-dialkylaminonaphthalene diimides by varying a linker between the imide nitrogen and a thiophene group”, J. Phys. Chem. C., 2014, 118, 3433-3442.

  39. Etheridge, F. S.; Fernando, R.; Sauve, G. "Tuning Optoelectronic Properties of core-Substituted Naphthalene Diimide Derivatives by Conversion of Carbonyl to Thiocarbonyl" 3rd Annual Symposium on Advances in Organic Photovoltaics, Kent State University, Kent, OH; April 16th, 2014; Submitted Poster.

  40. Daddario, C.; Han, Q.; Mao, Z.; Sauve, G.  "Azadipyrromethene-based Dyes for Organic Solar Cell Applications: Effect of Ethynylthiophene Substitution at the Distal or Proximal Phenyls."  ACS Dallas Conference, Division of Inorganic Chemistry, Molecular Inorganic Chemistry at the Frontiers of Energy Research, Dallas, Texas, March 16-20, 2014; Submitted poster.

  41. Wei Huang, Krishna M Ravikumar, and S. Yang, A Newfound Cancer-activating Mutation Reshapes the Energy Landscape of Estrogen-binding Domain J. Chem. Theory Comput. ASAP article, doi:10.1021/ct500313e (2014).

  42. S. Yang, Methods for SAXS-based Structure Determination of Biomolecular Complexes Advanced Materials (impact factor: 14.8), published nline, doi: 10.1002/adma.201304475 (2014). 
  43. Sparks, R, Bloch, N, Moses, D, Ponsky, L, Barratt, D, Feleppa, E, Madabhushi, A, “Multi-Attribute Probabilistic Prostate Elastic Registration (MAPPER): Application to Fusion of Ultrasound and Magnetic Resonance Imaging”, Medical Physics,  Mar;42(3):1153-63. doi: 10.1118/1.4905104. (PMID:25735270) 
  44. Tiwari, P, Shabbar, D, Madabhushi, A, “Identifying MRI Markers Associated with Early Response following Laser Ablation for Neurological Disorders: Preliminary Findings”, PLoS One. 2014 Dec 11;9(12):e114293. doi: 10.1371/journal.pone.0114293. eCollection 2014. (PMID: 25503713). 
  45. Ali, S, Veltri, R, Epstein, J, Christudas, C, Madabhushi, A, “Selective Invocation of Shape Priors for Deformable Segmentation and Morphologic Classification of Prostate Cancer Tissue Microarrays”, Comput Med Imaging Graph. 2014 Nov 12. pii: S0895-6111(14)00176-1. doi: 10.1016/j.compmedimag.2014.11.001. [Epub ahead of print] (PMID:25466771). 
  46. Colen, R, Foster, I, Gatenby, R, Giger, M, Gillies, R, Gutman, D, Heller, M, Jain, R, Madabhushi, A, Madhavan, S, Napel, S, Rao, A, Saltz, J, Tatum, J, Verhaak, R, Whitman, G, “NCI Workshop Report: Clinical and Computational Requirements for Correlating Imaging Phenotypes with Genomics Signatures,” Translational Oncology, vol. 7[5], pp. 556-569, 2014 (PMID: 25389451). 
  47. Litjens, G, Huisman, H, Elliot, R, Shih, N, Feldman, M, Viswanath, S, Futterer, J, Bomers, J, Madabhushi, A, “Quantitative identification of MRI features of prostate cancer response following laser ablation and radical prostatectomy”, Journal of Medical Imaging, vol. 1(3):035001. doi: 10.1117/1.JMI.1.3.035001, 2014 (PMID:26158070). 
  48. Wang, H, Cruz, A, Basavanhally, A, Gilmore, H, Shih, N, Feldman, M, Tomaszewski, J, Gonzalez, F, Madabhushi, A, “Mitosis Detection in Breast Cancer Pathology Images by Combining Handcrafted and Convolutional Neural Network Features”, J. Med. Imag., 1(3):034003. doi: 10.1117/1.JMI.1.3.034003, 2014 (PMID:26158062) 
  49. Lee, G, Singanamalli, A, Wang, H, Feldman, M, Master, SR, Shih, N, Spangle, E, Rebbeck, T, Tomaszewski, J, Madabhushi, A, “Supervised Multi-View Canonical Correlation Analysis (sMVCCA): Integrating histologic and proteomic features for predicting recurrent prostate cancer”, IEEE Transactions on Medical Imaging, IEEE Trans Med Imaging, 2014,  (PMID: 25203987). 
  50. Ginsburg, S, Bloch, BN, Genega, E, Lenkinsky, R, Feleppa, E, Rofsky, N, Madabhushi, A, “A Novel PCA-VIP Scheme for Ranking MRI Protocols and Identifying Computer Extracted MRI Measurements Associated with Central Gland and Peripheral Zone Prostate Tumors”, Journal of Magnetic Resonance Imaging, 2014. doi: 10.1002/jmri.24676. (PMID: 24943647). 
  51. Rusu, M, Bloch, BN, Jaffe, C, Genega, E, Lenkinsky, R, Feleppa, E, Rofsky, N, Madabhushi, A, “Prostatome: A combined anatomical and disease based MRI atlas of the prostate”, Medical Physics, vol. 41[7], pg. 072301, 2014 (PMID: 24989400). 
  52. Lee, GSparks, RAli, S, Feldman, M, Master, S, Shih, N, Tomaszewski, J, Madabhushi, A, “Co-occurring Gland Tensors in Localized Subgraphs: Predicting Biochemical Recurrence in Intermediate-risk Prostate Cancer Patients”, PLOS ONE, vol. 9[5], e97954, 2014 (PMID: 24875018). 
  53. Viswanath S, Sperling D, Lepor H, Futterer J, Madabhushi A “Identifying Quantitative In Vivo Multi-Parametric MRI Features For Treatment Related Changes after Laser Interstitial Thermal Therapy of Prostate Cancer” Neurocomputing, Special Issue on Image Guided Interventions, vol. 144, pp. 13-23, 2014 (PMID: 25346574). 
  54. Wan, TMadabhushi, A, Phinikaridou, A, Hamilton, J, Hua, N, Pham, T, Danagoulian, J, Buckler, A, “Spatio-temporal texture (SpTeT) for distinguishing vulnerable from stable atherosclerotic plaque on DCE-MRI in a rabbit model”, Medical Physics, vol. 41[4], pg. 042303, 2014 (PMID: 24694153). 
  55. Veta, M, van Diest, PJ, Willems, SM, Wang, H, Madabhushi, A, Cruz-Roa, A, Gonzalez, F, Larsen, ABL, Vestergaard, JS, Dahl, AB, Cireșan, DC, Schmidhuber, J, Giusti, A, Gambardella, LM, Tek, FB, Walter, T, Wang, CW, Kondo, S, Matuszewski, BJ, Precioso, F, Snell, V, Kittler, J, de Campos, TE, Khan, AM, Rajpoot, NM, Arkoumani, E, Lacle, MM, Viergever, MA, Pluim, JPW, “Assessment of algorithms for mitosis detection in breast cancer histopathology images”, Medical Image Analysis, 2014 Nov 29. pii: S1361-8415(14)00180-7. doi: 10.1016/ [Epub ahead of print] (PMID:25547073)
  56.  Mark Turner, “The Future of Computational Creativity.” UNAM (National Autonomous University of México). 31 October 2014.
  57. Mark Turner, “Research in the Red Hen Lab.” UAM (Autonomous Metropolitan University at Cuajimalma, México). 30 October 2014. 
  58. Mark Turner, “Computational Creativity and Blending.” UAM (Autonomous Metropolitan University at Cuajimalma, México). 28 October 2014.
  59. Mark Turner, “Computational Creativity through Conceptual Integration.” PROSECCO European Contact Forum on Computational Creativity. El Escorial, Real Colegio Universitario Maria Cristina. 21-23 February 2014. 


  1. John T. GiblinJr., James B. Mertens, Vacuum bubbles in the presence of a relativistic fluid, Journal of High Energy Physics, December 2013, 2013:42
  2. Patel VN, Gokulrangan G, Chowdhury SA, Chen Y, Sloan AE, Koyutürk M, Barnholtz-Sloan J, Chance MR. Network signatures of survival in glioblastoma multiforme. PLoS Comput Biol. 2013;9(9):e1003237. doi: 10.1371/journal.pcbi.1003237. Epub 2013 Sep 19. PubMed PMID: 24068912; PubMed Central PMCID: PMC3777929.
  3. Vengoechea J, Sloan AE, Chen Y, Guan X, Ostrom QT, Kerstetter A, Capella D, Cohen ML, Wolinsky Y, Devine K, Selman W, Barnett GH, Warnick RE, McPherson C, Chiocca EA, Elder JB, Barnholtz-Sloan JS. Methylation markers of malignant potential in meningiomas. J Neurosurg. 2013 Oct;119(4):899-906. doi: 10.3171/2013.7.JNS13311. Epub 2013 Aug 9. PubMed PMID: 23930849.
  4. Jagodnik K, van den Bogert A, Blana D, Kirsch R (2013) Toward the Restoration of Voluntary Arm Movement in High-Level Spinal Cord Injury: An Optimized Feedback Controller for a 3-Dimensional Arm. Poster Presentation at ShowCASE, April 12, 2013, Case Western Reserve University, Cleveland, Ohio.
  5. Electronic band structure, phonons, and exciton binding energies of halide perovskites CsSnCl3, CsSnBr3, and CsSnI3, Ling-yi Huang and Walter R. L. Lambrecht, Phys. Rev. B 88, 165203 (2013) - Published 17 October 2013
  6. Strain effects on the spin-orbit-induced band structure splittings in monolayer MoS2 and graphene, Tawinan Cheiwchanchamnangij, Walter R. L. Lambrecht, Yang Song, and Hanan Dery, Phys. Rev. B 88, 155404 (2013) - Published 7 October 2013
  7. Band offsets between ZnGeN2, GaN, ZnO, and ZnSnN2 and their potential impact for solar cells, Atchara Punya and Walter R. L. Lambrecht, Phys. Rev. B 88, 075302 (2013) - Published 2 August 2013
  8. J. Uddin and A. B. Anderson, "Trends with coverage and pH in Stark tuning rates for CO on Pt(111)", Electrochim. Acta 108, 398-403 (2013),

  9. S. Gajurel and R. Bielefeld, "Fast Vertex Cover Algorithms and Its Implementation using CWRU High Performance Computing Cluster (HPCC)", Poster Presentation at Research ShowCase 2013. Link to poster

  10. Sahoo S, Jayapandian C, Garg G, Kaffashi F, Chung S, Bozorgi A, Chen CH, Loparo K, Lhatoo SD, and Zhang GQ.
    Heart beats in the cloud: distributed analysis of electrophysiological 'big data' using cloud computing for epilepsy clinical research. Journal of the American Medical Informatics Association (2013). [PMID: 24326538]

  11. Jayapandian CP, Chen CH, Bozorgi A, Lhatoo SD, Zhang GQ, Sahoo SS.
    Cloudwave: Distributed Processing of “Big Data” from Electrophysiological Recordings for Epilepsy Clinical Research Using Hadoop. American Medical Informatics Association (AMIA) Annual Symposium, 2013. pp. 691-700.

  12. Huang, W., Greene, G.L., Ravikumar, K., and Yang, S. "Cross-talk between the ligand- and DNA-binding domains of estrogen receptor," Proteins. doi: 10.1002/prot.24331 (2013). [Applied multiscale simulations for the energy landscape of a multidomain protein complex]

  13. Ravikumar, K., Huang, W., and Yang, S. "Fast-SAXS-pro: A unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes," J. Chem. Phys. 138 (2) 024112, (2013) [Developed a new SAXS computing algorithm for protein-DNA/RNA complexes]

  14. Yang, S.*, Ravikumar, K., Levine, H.* "Energy evaluation of β-strand packing in a fibril-forming SH3 domain," J. Phys. Chem. B. doi: 10.1021/jp402442p (2013). [*Corr authors]

  15. Toth, R., Traghber, B., Ellis, R., Kurhanewicz, J., Madabhushi, A. “Registration of Pre and Post Intensity Modulated Radiation Therapy Prostate MRI for Quantification of MR Imaging Marker Changes and Precise Local Prostate Deformations,” at: Research ShowCASE, Case Western Reserve University, Cleveland, OH, Apr 2013.

  16. Toth, R., Ribault, J., Gentile, J.C., Sperling, D., Madabhushi, A. “Simultaneous Segmentation of Prostatic Zones Using Active Appearance Models with Multiple Coupled Levelsets,” CVIU Special Issue on Shape Modeling, April 2013. doi: 10.1016/j.cviu.2012.11.013.

  17. Toth, R., Kurhanewicz, J., Madabhushi, A. “Registration of Pre and Post Intensity Modulated Radiation Therapy Prostate MRI for Quantification of MR Imaging Marker Changes and Precise Local Prostate Deformations” ISMRM 2013.

  18. Singanamalli A., Sparks R., Rusu M., Shih N., Ziober A., Tomaszewski J., Rosen M., Feldman M, and Madabhushi A. "Radiohistomorphometric Image Analysis and Coregistration Scheme to identify DCE MRI markers for prostate cancer aggressiveness." 2013 ShowCASE.

  19. Singanamalli A., Sparks R., Rusu M., Shih N., Ziober A., Tomaszewski J., Rosen M., Feldman M, and Madabhushi A. "Radiohistomorphometric Image Analysis and Coregistration Scheme to identify DCE MRI markers for prostate cancer aggressiveness." 2013 ISMRM.

  20. Haibo Wang, Anant Madabhushi, Discriminatively Weighted Multi-Scale Local Binary Patterns: Applications in Prostate Cancer Diagnosis on T2W MRI, ISBI (oral), 2013.

  21. Eileen Hwuang, Shabbar Danish, Mirabela Rusu, Robert Sparks, Robert Toth, Anant Madabhushi. Anisotropic Smoothing Regularization (AnSR) in Thirion's Demons Registration Evaluates Brain MRI Tissue Changes Post-Laser Ablation. Conf Proc IEEE Eng Med Biol Soc. 2013.

  22. Singanamalli, Asha, et al. "Identifying in vivo DCE MRI parameters correlated with ex vivo quantitative microvessel architecture: A radiohistomorphometric approach." SPIE Medical Imaging. International Society for Optics and Photonics, 2013.

  23. Mirabela Rusu, B. Nicolas Bloch, C. Carl Jaffe, Neil M. Rofsky, Elizabeth M. Genega, Robert E. Lenkinski, Anant Madabhushi; Statistical 3D prostate imaging atlas construction via anatomically constrained registration, SPIE Medical Imaging Feb 2013

  24. Mirabela Rusu, Haibo Wang, Thea Golden, Andrew Gow, Anant Madabhushi
    Multiscale, multimodal fusion of histological and MRI lung volumes for characterization of airways SPIE Medical Imaging Feb 2013

  25. Mirabela Rusu, B. Nicolas Bloch, Carl Jaffe, Neil Rofsky, Elizabeth Genega, Robert Lenkinski, Anant Madabhushi; Statistical 3D prostate imaging atlas construction via anatomically constrained registration; ShowCase Case Western Research University, April 12, 2013 Cleveland; *Postdoctoral Research Award

  26. Viswanath, S, Bloch, BN, Chappelow, J, Genega, E, Lenkinski, R, Rofsky, N, Madabhushi, A, “Comparing Classifier Ensembles for Discriminating Central Gland and Peripheral Zone Tumors on In Vivo 3 Tesla T2-weighted Prostate MRI”, BMC Bioinformatics (under review).

  27. Viswanath, S, Toth, R, Rusu, M, Sperling, D, Lepor, H, Futterer, J, Madabhushi, A, “Quantitative evaluation of treatment related changes on multi-parametric MRI after laser interstitial thermal therapy of prostate cancer”, SPIE Medical Imaging, 2013, vol 8671, 86711F.

  28. Viswanath, S, Toth, R, Rusu, M, Sperling, D, Lepor, H, Futterer, J, Madabhushi, A, “Quantitative Evaluation of Treatment Related Changes on Multi-Parametric MRI after Laser Interstitial Thermal Therapy of Prostate Cancer”, ISMRM, Apr 2013.

  29. Viswanath, S, Toth, R, Rusu, M, Sperling, D, Lepor, H, Futterer, J, Madabhushi, A, “Quantitative Evaluation of Treatment Related Changes on Multi-Parametric MRI after Laser Interstitial Thermal Therapy of Prostate Cancer“, Research ShowCASE, Case Western Reserve University, Cleveland, OH Apr 2013.

  30. A. B. Anderson, R. Jinnouchi, and J. Uddin, "Effective Reversible Potentials and Onset Potentials for O2 Electroreduction on Transition Metal Electrodes: Theoretical Analysis", J. Phys. Chem. C 117, 41-48 (2013).

  31. L. García Domínguez, J.L. Pérez Domínguez, R. F. Galán (2013). A Model of Functional Brain Connectivity and Background Noise as a Biomarker for Cognitive Phenotypes: Application to Autism. PLoS ONE 8(4): e61493.
    Link to article

  32. Villarreal SA, Williams DR, Johnson CH, Egli M, Stewart PL. (2013) Examining the S. elongatus KaiBC Complex by CryoEM and MDFF. Microscopy and Microanalysis Annual meeting presentation.

  33. Seth A. Villarreal, Rekha Pattanayak, Dewight R. Williams, Carl H. Johnson, Martin Egli, Phoebe L. Stewart. Modeling of the Circadian Clock KaiBC Complex. Poster Presentation at Research ShowCase 2013.

  34. Justin W. Flatt, Eric Irons, Konstantin Doronin, Tara L. Fox, Dmitry M. Shayakhmetov, and Phoebe L. Stewart Adenovirus Immunity: Insights from coagulation factor VII on how X marks the spot. Poster Presentation at Research ShowCase 2013.

  35. Flatt JW, Kim, R Smith JG, Nemerow GR, Stewart PL (2013). An intrinsically disordered region of the adenovirus capsid is implicated in neutralization by human alpha defensin 5. PLoS One, 8(4):e61571

  36. Guo, H.; Zehavi, I.; Zheng, Z.; Weinberg, D. H.; Berlind, A. A.; Blanton, M.; Chen, Y.; Eisenstein, D. J.; Ho, S.; Kazin, E.; Manera, M.; Maraston, C.; McBride, C. K.; Nuza, S. E.; Padmanabhan, N.; Parejko, J. K.; Percival, W. J.; Ross, A. J.; Ross, N. P.; Samushia, L.; Sánchez, A. G.; Schlegel, D. J.; Schneider, D. P.; Skibba, R. A.; Swanson, M. E. C.; Tinker, J. L.; Tojeiro, R.; Wake, D. A.; White, M.; Bahcall, N. A.; Bizyaev, D.; Brewington, H.; Bundy, K.; da Costa, L. N. A.; Ebelke, G.; Malanushenko, E.; Malanushenko, V.; Oravetz, D.; Rossi, G.; Simmons, A.; Snedden, S.; Streblyanska, A.; Thomas, D., "The Clustering of Galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: Luminosity and Color Dependence and Redshift Evolution", The Astrophysical Journal 2013, 767, 122-140

  37. Senevirathna, W.; Sauvé, G. "Introducing 3D conjugated acceptors with intense red absorption: homoleptic metal (II) complexes of di(phenylacetylene) azadipyrromethene", J. Mater. Chem. C, 2013, 1, 6684-6694.

  38.  Fernando, R.; Mao, Z.; Sauvé, G. "Rod-like oligomers incorporating 2,6-dialkylamino core-substituted naphthalene diimide as acceptors for organic photovoltaic" Org. Electron., 2013, 14, 1683-1692.

  39. Daddario, C.; Han, Q.; Mao, Z.; Sauve, G.  "Azadipyrromethene-based Dyes for Organic Solar Cell Applications: Effect of Ethynylthiophene Substitution at the Distal or Proximal Phenyls."  Ohio Inorganic Weekend, University at Dayton, Dayton, Ohio, November 15-16, 2013, Submitted poster.

  40. Fernando, R.; Mao, Z.; Sauve, G. "Core-substituted Naphthalene Diimide-based Macromolecules" Annual Symposium on Advances in Organic Photovoltaics, Kent State University, Kent, OH, United States, April 17, 2013; Submitted poster.


  1. Dazard J-E., Saha S., Ewing R.M. ROCS: A Reproducibility Index and Confidence Score for Interaction Proteomics Studies. BMC Bioinformatics (2012) 13(1) 128. PMCID: PMC3568013.

  2. 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.

  3. 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.

  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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
  12. Jayapandian CP, Chen CH, Bozorgi A, Lhatoo SD, Zhang GQ, Sahoo SS.
    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,, 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 2012116, 8718-8730. Link to article

  22. Yang, Y. "Metal–ligand coordination in subphthalocyanines and phthalocyanines: DFT, AIM and ELF analyses," Polyhedron 201233, 310-318. Link to article

  23. Yang, Y. "Pyrrolic macrocycles with stabilized triplet states: Metal-centered and ligand-centered separation of unpaired electrons," Polyhedron 201242, 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 PerspectiveBiophysical 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- altp-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.


  1. Dazard J-E., Xu H., Rao J.S. R package MVR for Joint Adaptive Mean-Variance Regularization and Variance Stabilization. In JSM Proceedings, Statistical Programmers and Analysts Section. Miami Beach, FL, USA. American Statistical Association-IMS (2011) p. 3849-3863. PMCID: PMC4725579.

  2. Barnholtz-Sloan JS, Guan X, Zeigler-Johnson C, Meropol NJ, Rebbeck TR. Decision tree-based modeling of androgen pathway genes and prostate cancer risk. Cancer Epidemiol Biomarkers Prev. 2011 Jun;20(6):1146-55. doi: 10.1158/1055-9965.EPI-10-0996. Epub 2011 Apr 14. PubMed PMID: 21493872; PubMed Central PMCID: PMC3111844.
  3. Jagodnik KM, Kirsch RF, Blana D, van den Bogert A (2011) Toward the Restoration of Voluntary Arm Movement in Human Spinal Cord Injury: An Optimized Feedback Controller for a Realistic 3D Arm Model. Poster Presentation at 2011 Veterans Administration Showcase, May 2 - 6, 2011, Cleveland, Ohio. 
  4. Jagodnik KM, Kirsch RF, Blana D, van den Bogert A (2011) Toward the Restoration of Voluntary Arm Movement in Human Spinal Cord Injury: An Optimized Feedback Controller for a Realistic 3D Arm Model. Poster Presentation at Biomedical Graduate Student Symposium, May 6, 2011, Case Western Reserve University, Cleveland, Ohio.
  5. Quasiparticle band structure of Zn-IV-N2 compounds, Atchara Punya, Walter R. L. Lambrecht, and Mark van Schilfgaarde, Phys. Rev. B 84, 165204 (2011) - Published 7 October 2011
  6. Peay, M. A.; Heckler, J. E.; Deligonul, N.; Gray, T. G. Organometallics 2011, 30, 5071–5074.

  7. Yang, Y.; Samas, B.; Kennedy, V. O.; Macikenas, D.; Chaloux, B. L.; Miller, J. A.; Speer, R. L.; Protasiewicz, J.; Pinkerton, A. A.; Kenney, M. E. Long, Directional Interactions in Cofacial Silicon Phthalocyanine Oligomers. J. Phys. Chem. A 2011115, 12474-12485. Link to article

  8. Yang, Y. Effects Induced by Axial Ligands Binding to Tetrapyrrole-Based Aromatic Metallomacrocycles. J. Phys. Chem. A 2011115, 9043-9054. Link to article

  9. Yang, Y. Electron localization in nonplanar conjugated macrocycles: Failure of electron buffers to delocalize electrons. Chem. Phys. Lett. 2011516, 268-271. Link to article
  10. Yang, Y. A theoretical study of experimentally unknown metallosubphthalocyanines. Chem. Phys. Lett. 2011511, 51-56. Link to article
  11. Steinke GK, Galán RF, 2011 Brain Rhythms Reveal a Hierarchical Network Organization. PLoS Comput Biol 7(10): e1002207. doi:10.1371/journal.pcbi.1002207. Link to article

  12. Yang, S. and Roux, B. "EROS: Better than SAXS!", Structure. 19 (1), 3-4 (2011). Link to article

  13. Feng Tian and Alfred B. Anderson, "Effective Reversible Potentials, Energy Loss and Overpotential on Platinum Fuel Cell Cathodes", J. Phys Chem. C, 115, 4076-4088 (2011). Link to article

  14. "The Quantity of Intracluster Light: Comparing Theoretical and Observational Measurement Techniques using Simulated Clusters", Rudick, C.S., Mihos, J.C., and McBride, C.K. (2011), The Astrophysical Journal, 732, 48. Link to article

  15. E. Allahyarov and P. L. Taylor "Simulation study of the equilibrium morphology in ionomers with different architectures" J. Polym. Sci. B, Pol. Phys. 49 368 (2011) Link to article

  16. E. Allahyarov and P. L. Taylor "Simulation study of field-induced proton-conduction pathways in dry ionomers" J. Phys.: Condens. Matter 23 234105 (2011). Link to article

  17. Cheiwchanchamnangij, T. & Lambrecht, W. R. L. Calculated x-ray linear dichroism spectra for Gd-doped GaN. Phys. Rev. B 84, 205119 (2011). Link to article

  18. Cheiwchanchamnangij, T. & Lambrecht, W. R. L. Band structure parameters of wurtzite and zinc-blende GaAs under strain in the GW approximation. Phys. Rev. B 84, 035203 (2011). Link to article

  19.  Gao, L.; Senevirathna, W.; Sauvé, G. “Azadipyrromethene-based conjugated oligomers with near-IR absorption and high electron affinity” Org. Lett. 2011, 13, 5354-5357. 


  1. Dazard J-E., Rao J.S. Regularized Variance Estimation and Variance Stabilization of High-Dimensional Data. In JSM Proceedings, High-Dimensional Data Analysis and Variable Selection Section. Vancouver, BC, Canada. American Statistical Association-IMS (2010) p. 5295-5309. PMCID: PMC4727967.
  2. Dazard J-E., Rao J.S. Local Sparse Bump Hunting. J. Comp Graph. Statistics (2010) 19(4): 900-929. PMCID: PMC3293195.

  3. Yang, Y. Hexacoordinate Bonding and Aromaticity in Silicon Phthalocyanine. J. Phys. Chem. A 2010114, 13257-13267. Link to article 
  4. Tivadar Orban, Grzegorz Bereta, Masaru Miyagi, Benlian Wang, Mark R. Chance, Marcelo Carlos Sousa, and Krzysztof Palczewski, "Conformational Changes in Guanylate Cyclase-Activating Protein 1 Induced by Ca2+ and N-Terminal Fatty Acid Acylation", Structure 18, 116–126 (2010). Link to article 
  5. Alfred. B. Anderson, ¿Theories for Predicting Reversible Potentials of Reactions on Electrode Surfaces from Internal and Gibbs Energies¿: Applications to ORR, ECS Transactions 28, 1-17 (2010). Link to article 
  6. K. A. Kurak and A. B. Anderson, “Selenium: a Nonprecious Metal Cathode Catalyst fort Oxygen Electroreduction”, J. Electrochem. Soc. 157, B173-B179 (2010). Link to article 
  7. Alfred B. Anderson, Jamal Uddin, and Ryosuke Jinnouchi, “Solvent Effects on OH(ads) Reduction on Pt(111) Electrodes”, under revision. 
  8. Elshad Allahyarov, Philip L. Taylor, and Harmut Löwen, "Simulation study of field-induced morphological changes in a proton-conducting ionomer", Phys. Rev. E 81, 031805 (2010). Link to article
  9. "The Formation and Evolution of Intracluster Light", conference talk by Craig Rudick at the 2010 Meeting of the American Astronomical Society, Washington, DC, January 2010. Link to article 
  10. Chen, Y., Eldho, N. V., Dayie, T. K., Carey, P.R., "Probing adenine rings and backbone linkages using base specific isotope-edited Raman spectroscopy: application to group II intron ribozyme domain V" Biochemistry, 49, 3427-35 (2010). Link to article 
  11. "Kinetic crystallography using Raman microscopy", Invited talk by Paul Carey to the American Crystallography Association, Chicago. July 2010.
  12. "The Raman revolution in structural biology", Invited talk by Paul Carey to the Int Conf Raman Spectrosc. Boston. August 2010. Link to article
  13. Y. Chen, P. Carey et al "Following RNA initiation in RNA Polymerase crystals by Raman microscopy", Poster at the meeting of the American Chem Soc, San Francisco, March 2010.
  14. Bo Gong, P. Carey, et al., "Measuring individual pKas in crystals of the Glms ribozyme be Raman crystallography", Poster at the meeting of the American Chem Soc, San Francisco, March 2010.
  15. S.-Y. Hsu and J.S. T’ien, “Flame spread over solids in buoyant and forced concurrent flows: Model computations and comparison with experiments,” 33rd International Symposium on Combustion, Beijing, China, Aug. 1-6, 2010.
  16. S.-Y. Hsu and J.S. T’ien, “Flame spread over solids in buoyant and forced concurrent flows: Model computations and comparison with experiments,” Proc. of Combust. Inst. 33, In Press. Link to article
  17. Ya-Ting Tseng, James S. T’ien: Limiting Length, Steady Spread and Non-growing Flames in Concurrent Flow over Solids, Journal of Heat Transfer, September 2010, Vol. 132, Issue 9. Link to article 
  18. M. Shoham, V. Khodaveridan*, M. Pesho*, B. Truitt*, L. Bollinger and P. Patel, Discovery of Antipathogenic Agents Against MRSA, 50th Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC), Boston, 12-15 September 2010, poster presentation 
  19. Wang, S.; Dormidontova, E. E.; Nanoparticle Design Optimization for Enhanced Targeting: Monte Carlo Simulations; Biomacromolecules, 2010, 11, 1785-1795. Link to article
  20. Wang, S.; Dormidontova, E. E.; Monte Carlo Simulation of Metallo-Supramolecular Micelles; Macromolecular Rapid Communications, 2010, 31, 897-903 Link to article
  21. Li, Z.; Dormidontova, E. E.  Kinetics of diblock copolymer micellization by dissipative particle dynamics; Macromolecules 2010, 43 3521. Lick to article
  22. Li, Z.; Djohari, H.; Dormidontova, E. E. Molecular dynamics simulations of supramolecular polymer rheology; J. Chem. Phys. 2010 accepted. Link to article
  23. Wang, S.; Hagy, M. C.; Dormidontova, E. E.; “Comparisons of polymer layer and nanoparticle targeting”, ACS National Meeting, March 2010, San Francisco CA
  24. Djohari, H.; Wang, S.; Dormidontova, E. E.; “Role of tether length in nanoparticle”, ACS National Meeting, March 2010, San Francisco CA
  25. Li, Z.; Dormidontova, E. E. Dissipative particles dynamics simulations of micellization kinetics, ACS National Meeting & Exposition, March 21, 2010 San Francisco, CA


  1. Y. Chen, P. L. Taylor, and D. A. Scherson "Electrochemical and In-Situ Optical Studies of Supported Iridium Oxide Films in Aqueous Solutions" J. Electrochem. Soc. 156 (1) F14-F21 (2009) Link to article
  2. E. Allahyarov and P. L. Taylor "Predicted field-induced hexatic structure in an ionomer membrane" Phys. Rev. E. 80 020801 (2009) Link to article
  3. E. Allahyarov, P. L. Taylor, and H. Löwen "Simulation study of sulfonate cluster swelling in ionomers" Phys. Rev. E. 80 061802 (2009) Link to article
  4. E. Allahyarov and P. L. Taylor, "Simulation Study of the correlation between structure and conductivity in stretched Nafion" J. Phys. Chem. B 113, 610-617 (2009)  Link to article
  5. K. Kamal, G. Mittal, and C.J. Sung, "Autoignition of n-Decane under Elevated Pressure and Low-to-Intermediate Temperature Conditions" Combustion and Flame 156, 1278-1288 (2009) Link to article
  6. X-L Yin and J Li, "A general graphical framework for detecting copy number variation" Accepted by Comput Syst Bioinformatics Conf (CSB2009) -
  7. X. Li and J. Li, "An almost linear time algorithm for a general haplotype solution on tree pedigrees with no recombination and its extensions" Journal of Bioinformatics and Computational Biology (JBCB), 7(3), 521-545 (2009) Link to article
  8. H. Djohari and E.E. Dormidontova, "Dissipative Particle Dynamics Simulations of Nanoparticle Targeting Dynamics" Poster at CWRU Research ShowCASE 2009
  9. H. Djohari and E.E. Dormidontova, "Dissipative Particle Dynamics Simulations of Micelle Targeting Dynamics" Central Regional Meeting of ACS, Cleveland, OH, May 2009
  10. H. Djohari and E.E. Dormidontova, "Kinetics of Nanoparticle Targeting by Dissipative Particle Dynamics Simulations" Biomacromolecules, available online (2009) -
  11. Gavin A. Buxton, Sandra L. Siedlak, George Perry and Mark A. Smith. There and Back Again: A Numerical Tale of Microtubule Dynamics. Submitted.
  12. Gavin A. Buxton, Alexander Alexeev, O. Berk Usta and Anna C. Balazs. Using Synthetic Cilia to Regulate the Transport of Microscopic Particles. Submitted.
  13. Rajat Ghosh, Gavin A. Buxton, O. Berk Usta, Anna C. Balazs, and Alexander Alexeev. Designing oscillating cilia that capture or release microscopic particles. Accepted in Langmuir.
  14. Ernest Durbin and Gavin A. Buxton. Controlling Drug Release using Responsive Polymer Core-Shell Nanoparticles. Submitted to Soft Matter: Responsive and Active Soft Materials issue.
  15. Gavin A. Buxton, N. Clarke and P. J. Hussey. Actin Dynamics and the Elasticity of Cytoskeletal Networks. Accepted in Express Polymer Letters.
  16. Gavin A. Buxton, Ultrathin, dynamic and groovy: the physics of Dutcher films. Annu. Rep. Prog. Chem., Sect. C: Phys. Chem. (2009)
  17. Yang J, Ma YQ, Page RC, Misra S, Plow EF, Qin J. Structure of an integrin alphaIIb beta3 transmembrane-cytoplasmic heterocomplex provides insight into integrin activation. Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17729-34. Epub 2009 Oct 1. PubMed PMID: 19805198; PubMed Central PMCID: PMC2764936.
  18. Kalp, M., Bethel. C. R., Bonomo, R. A. and Carey, P. R. "Why extended-spectrum beta-lactamases SHV-2 and SHV-5 are "hypersusceptible" to mechanism-based inhibitors". Biochemistry, 48, 9912-9920 (2009).
  19. Kalp, M., Totir, M. A., Buynak, J. D., and Carey, P. R. "Different intermediate populations formed by tazobactam, sulbactam, and clavulanate reacting with SHV-1 beta-lactamases: Raman crystallographic evidence." J. Amer. Chem. Soc, 131, 2338-2347 (2009).
  20. Qingfu Feng, Joseph Abraham, Tao Feng, Yeunjoo Song, Robert C Elston, Xiaofeng Zhu, BMC Genetics. In press
  21. “Predicting Reversible Potentials of Reactions on Electrode Surfaces from Internal and Gibbs Energies”, Talk given by A. B. Anderson, at the 38th Great Lakes Regional Meeting of the American Chemical Society, Lincolnshire Il May13-16, 2009.
  22. “Theories for Predicting Reversible Potentials of Reactions on Electrode Surfaces from Internal and Gibbs Energies: Applications to ORR”, talk given by A. B. Anderson at Brookhaven National Laboratory, August 26, 2009.
  23. “Theories for Predicting Reversible Potentials of Reactions on Electrode Surfaces from Internal and Gibbs Energies: Applications to ORR”, talk given by A. B. Anderson at the Pittsburgh-Cleveland Catalysis Society Meeting, October 9, 2009.
  24. "Theory for Coverage Dependence of Reversible Potential for H2O Oxidation on Pt(111) in Acid", F. Tian, and A. B. Anderson, poster presentation at the 215th Electrochemical Society Meeting, San Francisco CA May 24-29, 2009.
  25. “Electroreduction of O2 on Selenium Nanotubes: Theoretical Prediction”, K. A. Kurak and A. B. Anderson, poster presentation at the 215th Electrochemical Society Meeting, San Francisco CA May 24-29, 2009.
  26. F. Tian, R. Jinnouchi, and A. B. Anderson, “How Potentials of Zero Charge and Potentials for Water Oxidation to OH(ads) on Pt(111) Electrodes Vary With Coverage”, J. Phys. Chem. C 113, 17484-17492 (2009).
  27. Rudick, C.S., Mihos, J.C., Frey, L.H. , and McBride, C.K., "Tidal Streams of Intracluster Light", The Astrophysical Journal, 699, 1518 (2009)
  28. Elshad Allahyarov and Philip L. Taylor, "Predicted electric-field-induced hexatic structure in an ionomer membrane", Phys. Rev. E 80, 020801(R) (2009)
  29. Elshad Allahyarov, Philip L. Taylor, and Hartmut Löwen, "Simulation study of sulfonate cluster swelling in ionomers", Phys. Rev. E 80, 061802 (2009)
  30. Morris NJ, Elston RC and Stein CM. “Calculating Asymptotic Significance Levels of the Constrained Likelihood Ratio Test with Application to Multivariate Genetic Linkage Analysis.” Statistical Applications in Genetics and Molecular Biology, v. 8 issue 1, 2009, p. 39.
  31. Morris NJ, Elston RC and Stein CM (2009) Robust Score Tests for Multivariate Linkage Analysis. Poster presentation at the 2009 Meeting of the American Society of Human Genetics.
  32. S.J. Fleming, H.F. McGinnis, S. Sarkar, H. Baskaran, & P.J. Thomas. "Analysis of gradient sensing based on maximum likelihood." Poster presented to conference of the Society for Mathematical Biology.  Vancouver, Canada. July 2009. 
  33. "Using Intracluster Light to Weigh Galaxy Clusters", conference talk by Chris Mihos at the international conference "Unveiling the Mass: Extracting and Interpreting Galaxy Masses", Kingston, Ontario, June 2009.
  34. Kalp, M., Buynak, J. D. and Carey, P. R. "Role of E166 in the Imine to Enamine Tautomerism of the Cllinical beta-Lactamase Inhibitor Sulbactam" Biochemistry, (2009) 48, 10196-98.
  35. Guo, M., Spitale, R. C., Volpini, R., Krucinska, J., Cristalli, G., Carey, P. R., and Wedekind, J. E. "Direct Raman Measurement of an Elevated Base pKa in the Active Site of a Small Ribozyme in a Pre-Catalytic Conformation" J. Amer. Chem. Soc., (2009) 131, 12908-9.
  36. Chen, J.-H., Gong, B., Bevilacqua, P. C., Carey, P. R., and Golden, B. L. "A Catalytic Metal Interacts with the Cleavage Site G.U Wobble in the HDV Ribozyme" Biochemistry, (2009) 48, 498-507.
  37. Gong, B., Chen, J.-H., Yajima, R., Chen, Y., Chase, E., Chadalavada, D. M., Golden, B. L., Carey, P. R., Bevilacqua, P. C. "Raman crystallography of RNA" Methods, (2009)
  38. Gong, B., Chen, J. H.,  Golden, B. L., Bevilacqua, P. C., and Carey, P. R. “Competition Between Co(NH3)63+and Inner-sphere Mg2+in the HDV Ribozyme”. Biochemistry., (2009) 48: 11961-70
  39. Y.-T. Tseng and J. S. T'ien: The Effect of Different Pyrolysis Descriptions on flame spread over Solids in Concurrent Flows, 6th U.S. National Combustion Meeting, Ann Arbor, Michigan 2009
  40. S.-Y. Hsu, Y.-T. Tseng and J.S. T’ien, “Modeling flame spread and extinction of solids in space exploration atmospheres,” International Conference on Environmental Systems, Fire Safety in Spacecraft and Enclosed Habitats, 09ICES-0333/2009-01-2492, 2009
  41. Kyle E. Niemeyer, Chih-Jen Sung, Mandhapati P. Raju, "Skeletal mechanism generation for surrogate fuels using directed relation graph with error propagation and sensitivity analysis," Combustion and Flame 57 (2010) 1760-1770. doi:10.1016/j.combustflame.2009.12.0
  42. G. Karl Steinke and Roberto F. Galán (2009). Reverse-engineering neural network topology from large-scale recording dynamics. Program No. 895.15. 2009 Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience, 2009. Online. SfN 39th Annual Meeting, October 17-21, 2009.
  43. G. Karl Steinke and Roberto F. Galán (2009). Inferring large-scale brain connectivity from spectral properties of the EEG. Computational Neuroscience Meeting, CNS 2009, Berlin, Germany.


  1. J. Li, "Prioritize and Select SNPs for Association Studies with Multi-stage Designs" Journal of Computational Biology. 15, 241–57 (2008)
  2. J. Li, and Y. Chen, "Generating samples for association studies based on HapMap data" BMC Bioinformatics 9, 44, 2008
  3. X. Zheng, P.L. Wintrode, and M.R. Chance, "Complementary Structural Mass Spectrometry Techniques Reveal Local Dynamics in Functionally Important Regions of a Metastable Serpin" Structure 16, 38-51 (2008)
  4. M.B. Hamaneh and P.L. Taylor, "Simulated anchoring of a nematic liquid crystal at a polymer surface" Physical Review E 77, 021707 (2008)
  5. Elshad Allahyarov, "Macrophase Ordering in Ionomers Under External Potential" Poster at CWRU Research ShowCASE 2008
  6. Zhenlong Li, Matthew C. Hagy, and Elena E. Dormidontova, "Dynamics of Amphiphile Self-assembly by DPD simulation" Poster at CWRU Research ShowCASE 2008
  7. Tula Paudel, "Theoretical study of native defects in Cadmium Germanium Arsenide" Poster at CWRU Research ShowCASE 2008
  8. P.L. Wintrode, "Exploring the link between folding, dynamics and metastability in human serpins" Gordon Research Conference on Biopolymers, Newport, RI, 2008
  9. N. Duff, E.K. Mann, and D.J. Lacks, "Molecular Dynamics Investigation of the Effects of a Water Surface on the Aggregation of Bent-Core Molecules" Langmuir 24, 4456 (2008)
  10. K. Forward, D.J. Lacks, and R.M. Sankaran, "Triboelectric Charging of Binary Granular Mixtures due solely to Particle-Particle Interactions" Electrostatics Society of America Annual Conference, Minneapolis, MN, June 2008
  11. X. Zheng, P.L. Wintrode, and M.R. Chance, "Complementary structural mass spectrometry techniques reveal local dynamics in functionally important regions of a metastable serpin" Structure 16, 1-14 (2008)
  12. Y. Tong, P.K. Hota, M.B. Hamaneh, and M. Buck, "Insights into Oncogenic Mutations of plexin-B1 based on the Solution Structure of the Rho GTPase Binding Domain Structure" Structure 16, 246-258 (2008)
  13. M.B. Hamaneh and P.L. Taylor, "Simulated Anchoring of a Nematic Liquid Crystal at a Polymer Surface" Virtual Journal of Biological Physics Research 15 (5) March 1, 2008
  14. E. Allahyarov and P. L. Taylor, “Correlation between structure and conductivity of stretched Nafion”, J. Phys. Chem. (submitted)
  15. M.B. Hamaneh and P.L. Taylor, "Simulated Anchoring of a Nematic Liquid Crystal at a Polymer Surface" Virtual Journal of Nanoscale Science & Technology 17 (11) March 17, 2008
  16. J. Zhu and X. Zhang, "Efficient VLSI architecture for soft-decision decoding of Reed-Solomon codes" to appear IEEE Trans. on Circuits & Systems –I, 2008.
  17. J. Zhu and X. Zhang, "Backward interpolation for algebraic soft-decision Reed-Solomon decoding" submitted to IEEE Trans. On VLSI Systems, Mar. 2008.
  18. J. Zhu, X. Zhang and Z. Wang, "Combined interpolation architecture for soft-decision decoding of Reed-Solomon codes" IEEE Conference on Computer Design, May 2008.
  19. G. Mittal, M.P. Raju, and C.J. Sung, "Computational Fluid Dynamics Modeling of a Rapid Compression Machine with Creviced Piston: Influence of Physical and Operating Parameters on its Performance" submitted.
  20. K. Kumar, G. Mittal, C.J. Sung, and C.K. Law, "An Experimental Investigation on Ethylene/O2/Diluent Mixtures: Laminar Flame Speeds with Preheat and Ignition Delays at High Pressures" Combustion and Flame 153, 343-354 (2008).
  21. G. Mittal, M.P. Raju, and C.J. Sung, "Computational Fluid Dynamics Modeling of Hydrogen Ignition in a Rapid Compression Machine" Combustion and Flame 155(3), 417-428, (2008)
  22. G. Mittal and C.J. Sung, “Homogeneous Charge Compression Ignition of Binary Fuel Blends,” Combustion and Flame 155, 431-439 (2008)
  23. M.P. Raju, and J.S. T’ien, "Modeling of candle burning with a self-trimmed wick" Combustion Theory and Modelling 12 (2), 367-388 (2008)
  24. M.P. Raju, and J.S. T’ien, "Development of Direct Multifrontal Solvers for Combustion Problems" Numerical Heat Transfer, Part B: Fundamentals 53(3), 189-205 (2008)
  25. M.P. Raju, and J.S. T’ien, "Two-Phase Flow inside an Externally Heated Axisymmetric Porous Wick" Journal of Porous Media 11(8), 701-718 (2008)
  26. J. Kleinhenz, I.I. Feier, S.Y. Hsu, J.S. T’ien, P.V. Ferkul, and K.R. Sacksteder, "Pressure modeling of upward flame spread and burning rates over solids in partial gravity" Combustion and Flame 154, 637-643 (2008)
  27. J. Zhu, X. Zhang and Z. Wang, "Backward interpolation for algebraic soft-decision Reed-Solomon decoding" IEEE Trans. on VLSI Systems, in press.
  28. Gavin A. Buxton, The Fate of a Polymer Nanoparticle Subject to Flow-Induced Shear Stresses. Europhys. Lett. 84 26006 (2008).
  29. Kalp, M. and Carey, P. R. "Carbapenems and SHV-1 beta-lactamase form different acyl-enzyme populations in crystals and solution", Biochemistry, 47, 11830-11837 (2008). 
  30. Totir M.A., Cha, J., Wang B., Sheri, A., Anderson, V.E., Buynak J., Mobashery, S., and Carey, P.R. “Why tazobactam and Sublactam Are Poor Inhibitors of OXA-10 β-Lactamase: Raman Crystallographic Evidence” Biochemistry, (2008) 47, 4094-4101.
  31. Gong, B., Chen, Y., Christian, E. L., Chen, J.-H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, Carey, P. R., J. Amer. Chem. Soc. 130, 9670-9672 (2008).


  1. P. Larson, Walter R.L. Lambrecht, Athanasios Chantis, and Mark van Schilfgaarde, "Electronic structure of rare-earth nitrides using the LSDA+U approach: Importance of allowing 4f orbitals to break the cubic crystal symmetry" Phys. Rev. B 75, 045114 (2007)
  2. M.B. Hamaneh and P.L. Taylor, "Range of Interlayer Interactions in Smectic-C Liquid Crystals" Phys. Rev. E 75, 011703 (2007)
  3. Mehdi Bagheri Hamaneh and Matthias Buck, "Acceptable Protein and Solvent Behavior in Primary Hydration Shell Simulations of Hen Lysozyme" Biophysical Journal 92, L49-L51 (2007)
  4. Chandrima Mitra and Walter R. Lambrecht, "Band-gap bowing in AgGa(Se1-xTex)2 and its effect on the second-order response coefficient and refractive indices" Phys. Rev. B 76, 205206 (2007)
  5. Chandrima Mitra and Walter R. Lambrecht, "Large band-gap bowing in Cu1−xAgxGaS2 chalcopyrite semiconductors and its effect on optical parameters" Phys. Rev. B 76, 035207 (2007)
  6. Pavel Lukashev, Walter R. Lambrecht, Takao Kotani, and Mark van Schilfgaarde, "Electronic and crystal structure of Cu2-xS : Full-potential electronic structure calculations" Phys. Rev. B 76, 195202 (2007)
  7. Tula R. Paudel and Walter R. Lambrecht, "First-principles calculation of the zone center phonons in ZnSiN2: Comparison with infrared data" Phys. Rev. B 76, 115205 (2007)
  8. M. S. Miao and Walter R. Lambrecht, "Effects of vacancies and impurities on the relative stability of rocksalt and zincblende structures for MnN" Phys. Rev. B 76, 195209 (2007)
  9. J.M. Kimmel, R. M. Salter, and P.J. Thomas, "An Information Theoretic Framework for Eukaryotic Gradient Sensing", Advances in Neural Information Processing Systems 19, MIT Press, pp 705-712, 2007
  10. Elshad Allahyarov and Philip L. Taylor. "Role of electrostatic forces in cluster formation in a dry ionomer" The Journal of Chemical Physics 127, 154901 (2007)
  11. Elshad Allahyarov, "Conformational Structures in Dry Ionomers" Poster at CWRU Research ShowCASE (2007).
  12. K. Kumar, J.E. Freeh, C.J. Sung, and Y. Huang, "Laminar Flame Speeds of Preheated iso-Octane/O2/N2 and n-Heptane/O2/N2 Mixtures" Journal of Propulsion and Power 23 (2), 428-436 (2007).
  13. G. Mittal and C.J. Sung, "Autoignition of Toluene and Benzene at Elevated Pressures in a Rapid Compression Machine" Combustion and Flame 150, 355-368 (2007).
  14. K. Kumar and C.J. Sung, "Laminar Flame Speeds and Extinction Limits of Preheated n-Decane/O2/N2 and n-Dodecane/O2/N2 Mixtures" Combustion and Flame 151, 209-224 (2007).
  15. Y. Huang, C.J. Sung, and K. Kumar, "Ultra-Dilute Combustion of Primary Reference Fuels" Combustion Science and Technology 179 (11), 2361-2379 (2007).
  16. S.Y. Hsu, and J.S. T’ien, "Effect of Chemical Kinetics on Concurrent-flow Flame Spread over Solids: A Comparison between Buoyant flow and Forced Flow Cases" IMECE2007-42293, ASME INTERNATIONAL MECHANICAL ENGINEERING CONGRESS AND EXPOSITION, Seattle, WA, November 11-15 2007.
  17. Y.T. Tseng, and J.S. T’ien, "Limiting Length and Non-growth of Flames in Concurrent Flow over Thick Solids" Eastern States Meeting/Combustion Institute, Charlottesville, VA. Oct. 21-24, 2007.
  18. X. Li and J Li, "Comparisons of haplotype inference from pedigree data and population data" BMC Proceedings 1:S55, 2007.
  19. G. Mittal, M.P. Raju, C. J. Sung, and K. P. Kundu, "A Computational Fluid Dynamics Study of a Rapid Compression Machine" Fall Technical Meeting of the Eastern States Section of the Combustion Institute, University of Virginia, VA, 2007.
  20. M.P. Raju and C.J. Sung, "Optimization of Combustion Application Codes using Sparse Matrix Techniques" Fall Technical Meeting of the Eastern States Section of the Combustion Institute, University of Virginia, VA, 2007.
  21. K. Kumar, G. Mittal, and C.J. Sung, "Autoignition of n-Decane under High Pressure Conditions" Fifth Joint Meeting of the U.S. Sections of the Combustion Institute, San Diego, CA, 2007.
  22. X. Zhang, "Further exploring the strength of prediction in the factorization of soft-decision Reed-Solomon decoding" IEEE Trans. on VLSI Systems, vol. 15(7), pp. 811-820, Jul. 2007.
  23. J. Zhu and X. Zhang, "Efficient interpolation architecture for soft-decision Reed-Solomon decoding" Proc. of IEEE Workshop on Signal Processing Systems, pp. 663-668, Shanghai, China, Oct. 2007.
  24. Kalp, M., Sheri, A., Buynak, J.D., Bethel, C.R., Bonomo R.A., and Carey, P.R. “Efficient inhibition of class A and class D β-Lactamases by Michaelis complexes.” J. Biol. Chem. 282, 21588-91, 2007.
  25. M. Stetner, D.M. Taylor “Evaluating Synchrony Between Neurons as a Signal for Brain Computer Interfaces” Intersections SOURCE Symposium, Cleveland, OH, April 2007. (1st Place Winner, poster competition; engineering category)


  1. P. Larson and Walter R. L. Lambrecht, "Electronic structure of Gd pnictides calculated within the LSDA+U approach" Phys. Rev. B 74, 085108 (2006)
  2. P.L. Wintrode, "The dynamical properties of a metastable protein studied by molecular dynamics simulations and normal mode analysis" 1st Ohio Collaborative Conference on Bioinformatics, Athens, Ohio (2006).
  3. Walter R. L. Lambrecht and M. S. Miao. "Electronic driving force for stacking fault expansion in 4H-SiC" Phys. Rev. B 73, 155312 (2006)
  4. N. Duff, D. J. Lacks, J. Wang and E. K. Mann, "Molecular simulation of the self-assembly of bent-core molecules at water surfaces", Midwest Thermodynamics and Statistical Mechanics Conference, Akron, OH, May 2006.
  5. N. Duff, J. Wang, E.K. Mann, and D.J. Lacks, "Molecular Dynamics Investigation of Bent-Core Molecules on a Water Surface" Langmuir 22, 9082 (2006).
  6. M. S. Miao and Walter R. Lambrecht, "Electronic structure and magnetic properties of transition-metal-doped 3C and 4H silicon carbide" Phys. Rev. B 74, 235218 (2006)
  7. N. Duff and D. J. Lacks, "Mechanical Properties of Proteins: the Dynamic Energy Landscape" AIChE Annual Meeting, San Francisco, CA, November 2006.
  8. N. Duff, D. J. Lacks, J. Wang and E. K. Mann "Molecular simulation of the self-assembly of bent-core molecules at water surfaces" AIChE Annual Meeting, San Francisco, CA, November 2006.
Sanjaya Gajurel,
May 15, 2014, 8:17 AM
Sanjaya Gajurel,
Oct 6, 2015, 8:37 AM
Sanjaya Gajurel,
Aug 14, 2015, 2:00 PM
Sanjaya Gajurel,
Sep 9, 2015, 9:01 AM
Sanjaya Gajurel,
Nov 11, 2014, 12:15 PM
Sanjaya Gajurel,
Apr 16, 2013, 8:23 AM