Publications


Book, Book Chapter, and Conference Proceedings

  1. Casey A. Cole, D. Ishimaru, M. Hennig, H. Valafar. (2016). Structure Calculation of α,Α/β, β Proteins From Residual Dipolar Coupling Data Using Redcraft. In: H. R. Arabnia, Q. N. Tran (Eds.), Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology. Morgan Kaufmann, Imprint of Elsevier, Cambridge, MA, pp. 73–88

  2. A. Fahim, S. Irausquin, H. Valafar. (2016). nD-PDPA: n-Dimensional Probability Density Profile Analysis. In: H. R. Arabnia, Q. N. Tran (Eds.), Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology. Morgan Kaufmann, Imprint of Elsevier, Cambridge, MA, pp. 179–194.

  3. Valafar, H., Simin, M., Irausquin, S. (2012). A Review of REDCRAFT: Simultaneous Investigation of Structure and Dynamics of Proteins from RDC Restraints. Annual Reports on NMR Spectroscopy, 76, 23–66. doi:10.1016/B978-0-12-397019-0.00002-9

  4. Valafar, H., Irausquin, S. J. (2012). Structure and Dynamics of Proteins from Nuclear Magnetic Resonance Spectroscopy, Protein Structure. In E. Faraggi (Ed.). InTech. Doi:10.5772/38682, Chapter 2

  5. H.R. Arabnia, H. Valafar: Proceedings of the 2006 International Conference on Bioinformatics Computational Biology, BIOCOMP'06, Las Vegas, Nevada, USA, June 26-29, 2006 CSREA Press 2006

  6. F. Valafar, H. Valafar: Proceedings of The 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS 2005, Las Vegas, Nevada, USA, June 20-23, 2005, CSREA Press 2005

  7. F. Valafar, H. Valafar: Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine andBiological Sciences, METMBS '04, June 21-24, 2004, Las Vegas, Nevada, USA ISBN number: 1-932415-43-2 (470 pages). CSREA press, USA, 2004.

  8. F. Valafar, H. Valafar: Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS '03, June 23 - 26, 2003, Las Vegas, Nevada ISBN number: 1-932415-04-1 (518 pages). CSREA press, USA, 2003.

  9. Associate editor of the Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS). ISBN numbers: 1-892512-31-9 (Volume I, 600 pages), 1-892512-32-7 (Volume II, 315 pages), and 1-892512-33-5 (complete set, 915 pages). CSREA press, USA, 2002.

  10. Associate editor of the Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS). ISBN number: 1-892512-77-7 (523 pages). CSREA press, USA, 2001.

  11. Associate editor of the Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS). ISBN numbers: 1-892512-60-2 (Volume I, 408 pages), 1-892512-61-0 (Volume II, 346 pages), and 1-892512-62-9 (complete set, 754 pages). CSREA press, USA, 2000.

Journal Publications

  1. Sarah Hales, Gabrielle M Turner-McGrievy, Sara Wilcox, Rachel E Davis, Arjang Fahim, Michael Huhns, Homayoun Valafar. Trading pounds for points: Engagement and weight loss in a mobile health intervention. Digital Health (2017). Link

  2. David Oliver, Hao Ji, Piaomu Liu, Alexander Gasparian, Ellen Gardiner, Samuel Lee, Adrian Zenteno, Lillian Perynskaya, Mengqian Chen, Phillip Buckhaults, Eugenia Broude, Michael D Wyatt, Homayoun Valafar, Edsel Pena, and Michael Shtutman (2017). Identification of novel cancer therapeutic targets using a designed and pooled shRNA library screen. Nature: Scientific Reports 7, Article number: 43023 doi:10.1038/srep43023 Impact Factor: 5.228

  3. Turner-McGrievy GM, Hales S, Schoffman DE, Valafar H, Brazendale K, Weaver RG, Beets MW, Wirth MD, Shivappa N, Mandes T, Hebert JR, Wilcox S, Hester A, McGrievy MJ. Choosing between responsive-design websites versus mobile apps for your mobile behavioral intervention: Presenting four case studies. Translational Behavioral Medicine. Pract. Policy Res. (2016). doi:10.1007/s13142-016-0448-y Impact Factor: 2.189

  4. Hales, Sarah, Turner-McGrievy, Gabrielle, Wilcox, Sara, Fahim, Arjang, Davis, Rachel E, Huhns, Michael, Valafar, Homayoun. (2016). Social Networks for Improving Healthy Weight Loss Behaviors for Overweight and Obese Adults: A Randomized Clinical Trial of the Social Pounds Off Digitally (Social POD) Mobile App. International Journal of Medical Informatics. In Press, Accepted Manuscript. doi:10.1016/j.ijmedinf.2016.07.003 Impact Factor: 2.363

  5. Casey A. Cole, Rishi Mukhopadhyay, Hanin Omar, Mirko Hennig, and Homayoun Valafar. (2016). Structure Calculation and Reconstruction of Discrete-State Dynamics from Residual Dipolar Couplings. J. Chem. Theory Comput., 12 (4), pp 1408–1422. DOI: 10.1021/acs.jctc.5b01091 Impact Factor: 5.301

  6. Hales, Sarah, Turner-McGrievy, Gabrielle, Fahim, Arjang, Freix, Andrew, Wilcox, Sara, Davis, Rachel E, Huhns, Michael, Valafar, Homayoun. (2016).A Mixed-Methods Approach to the Development, Refinement, and Pilot Testing of Social Networks for Improving Healthy Behaviors. JMIR Human Factors. 3 (1). Link: http://humanfactors.jmir.org/2016/1/e8/ Impact Factor: 4.535

  7. Simin, M., Irausquin, S., Cole, C. A., Valafar, H. (2014). Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings. Journal of Biomolecular NMR. http://doi.org/10.1007/s10858-014-9871-x, PMID: 25403759 Impact Factor: 3.141

  8. Mukhopadhyay, R., Irausquin, S., Schmidt, C., Valafar, H. (2014). Dynafold: a dynamic programming approach to protein backbone structure determination from minimal sets of residual dipolar couplings. Journal of Bioinformatics and Computational Biology, 12(1), 1450002. http://doi.org/10.1142/S0219720014500024, PMID: 24467760 Impact Factor: 0.931

  9. Schmidt, C., Irausquin, S. J.,Valafar, H. (2013). Advances in the REDCAT software package. BMC bioinformatics, 14(1), 302. doi:10.1186/1471-2105-14-302, PMID: 24098943. (MCB-0644195) Impact Factor: 2.435

  10. Fahim, A., Mukhopadhyay, R., Yandle, R., Prestegard, J. H., Valafar, H. (2013). Protein Structure Validation and Identification from Unassigned Residual Dipolar Coupling Data Using 2D-PDPA. Molecules (Basel, Switzerland), 18(9), 10162–88. doi:10.3390/molecules180910162, PMID: 23973992. (MCB-0644195, P20 RR-016461) Impact Factor: 2.465

  11. Fawcett, T. M., Irausquin, S. J., Simin, M., Valafar, H. (2013). An artificial neural network approach to improving the correlation between protein energetics and the backbone structure. Proteomics, 13(2), 230–8. doi:10.1002/pmic.201200330, PMID: 23184572. (NIH-1R01GM081793, P20 RR-016461) Impact Factor: 4.079

  12. Shealy, P., Valafar, H. (2012). Multiple structure alignment with msTALI. BMC bioinformatics, 13(1), 105. doi:10.1186/1471-2105-13-105, PMID:22607234. (NIH-1R01GM081793, MCB-0644195) Impact Factor: 2.435

  13. Valafar, H., Simin, M., Irausquin, S. (2012). A Review of REDCRAFT: Simultaneous Investigation of Structure and Dynamics of Proteins from RDC Restraints. Annual Reports on NMR Spectroscopy, 76, 23–66. doi:10.1016/B978-0-12-397019-0.00002-9, Web access. (1R01GM081793, 5P20RR016461) Impact Factor: 2.129

  14. Valafar, H., Irausquin, S. J. (2012). Structure and Dynamics of Proteins from Nuclear Magnetic Resonance Spectroscopy, Protein Structure. In E. Faraggi (Ed.). InTech. Doi:10.5772/38682, Chapter 2, Web access. (NIH-1R01GM081793, MCB-0644195)

  15. Shealy P, Liu Y, Simin M, Valafar H., Backbone resonance assignment and order tensor estimation using residual dipolar couplings, J Biomol NMR. 2011 Jun 12, PMID:21667298. ( MCB-0644195 ) Impact Factor: 3.141

  16. Shealy P, Simin M, Park SH, Opella SJ, Valafar H, Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bound form of Pf1 Coat Protein, Journal of Magnetic Resonance 2010 Nov;207(1):8-16. Epub 2010 Jul 30, PMID:20829084( 1R01GM081793 ) Impact Factor: 2.889

  17. Park SH, Son WS, Mukhopadhyay R, Valafar H, Opella SJ., Phage-Induced Alignment of Membrane Proteins Enables the Measurement and Structural Analysis of Residual Dipolar Couplings with Dipolar Waves and lambda-Maps, J Am Chem Soc. 2009 Oct 14;131(40):14140-1, PMID:19761238( 1R01GM081793 ) Impact Factor: 13.038

  18. Mukhopadhyay R, Miao X, Shealy P, Valafar H, Efficient and accurate estimation of relative order tensors from λ-maps, J Magn Reson. Volume 198, Issue 2, June 2009, Pages 236-247, PMID:19345125. ( MCB-0644195 ) Impact Factor: 2.889

  19. Miao X, Mukhopadhyay R, Valafar H, Estimation of relative order tensors, and reconstruction of vectors in space using unassigned RDC data and its application, J Magn Reson. 2008 Oct;194(2):202-11, PMID:18692422. ( MCB-0644195 ) Impact Factor: 2.889

  20. Miao X, Waddell PJ, Valafar H, TALI: local alignment of protein structures using backbone torsion angles, J Bioinform Comput Biol. 2008 Feb;6(1):163-81, PMID:18324751. ( MCB-0644195 ) Impact Factor: 0.931

  21. Bansal S, Miao X, Adams MW, Prestegard JH, Valafar H, Rapid classification of protein structure models using unassigned backbone RDCs and probability density profile analysis (PDPA). J Magn Reson. 2008 Feb 12, PMID:18321742. ( MCB-0644195 ) Impact Factor: 2.889

  22. Bryson M, Tian F, Prestegard JH, Valafar H, REDCRAFT: A tool for simultaneous characterization of protein backbone structure and motion from RDC data. J Magn Reson. 2008 Apr;191(2):322-34, PMC2728087, PMID:18258464. ( 1R01GM081793 ) Impact Factor: 2.889

  23. Prestegard JH, Mayer KL, Valafar H, Benison GC., Determination of protein backbone structures from residual dipolar couplings, Methods Enzymol. 2005;394:175-209, PMC1808351, PMID:15808221 Impact Factor: 1.70

  24. Wang J, Valafar H, Prestegard JH, Assessment of protein alignment using 1H-1H residual dipolar coupling measurements, J Magn Reson, 2005 Jan;172(1):85-90, PMID:15589411 Impact Factor: 2.889

  25. Di Lello P, Benison GC, Valafar H, et al., NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyase involved in the bacterial mercury resistance system, BIOCHEMISTRY 43 (26): 8322-8332 JUL 6 2004, PMID:15222745 Impact Factor: 3.015

  26. Valafar H, Mayer KL, Bougault CM, LeBlond PD, Jenney FE Jr, Brereton PS, Adams MW, Prestegard JH, Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target, J Struct Funct Genomics. 2004;5(4):241-54, PMC1815388, PMID:15704012 Impact Factor: 2.48

  27. H. Valafar, Arabnia H.R., Distributed Global Optimization and its Potential Implementation on the MultiRing Network. Journal of Neural, Parallel and Scientific, Vol. 12, no. 4, pp. 465-490. Dec. 2004

  28. L. C. Morris, Valafar H., Prestegard J. H., Assignment of Backbone Resonances from Minimal NMR Data Using Connectivity, Torsion Angle Constraints, and Chemical Shifts. Journal of Biomolecular NMR 29: 1-9, 2004, PMID:15017135

  29. H. Valafar, Prestegard J.H., REDCAT: A Residual Dipolar Coupling Analysis Tool. Journal of Magnetic Resonance 167 (2004) 228-241, PMID:15040978

  30. K. Umemoto, Leffler H., Venot A., Valafar H., Prestegard J., Conformational Differences in Liganded and Unliganded States of Galectin-3. Biochemistry, 2 (13): 3688-3695 APR 8 2003, PMID:12667058

  31. H. Valafar, Presetegard J., Rapid Classification of a Protein Fold Family Using a Statistical Analysis of Dipolar Couplings. Bioinformatics, 2003 Aug 12:19(12):1549-55, PMID:12912836

  32. Ford MG, Valafar H, Prestegard JH, Utilizing molecular symmetry and dipolar couplings to assign the resonances of a 33kDa protein complex, BIOPHYSICAL JOURNAL 84 (2): 276A-276A Part 2 Suppl. S FEB 2003,

  33. H. Valafar, Valafar F., J. Prestegard, Data-mining protein structure databanks for crystallization patterns of proteins, Techniques in Bioinformatics and Medical Informatics, Annals of the New York Academy of Sciences, 980: 13-22 2002, PMID:12594078

  34. H. Valafar, Valafar F., Data Mining and Knowledge Discovery in Proton Nuclear Magnetic Resonance (1H-NMR) Spectra using Frequency to Information Transformation (FIT). KNOWL-BASED SYST 15 (4): 251-259 Sp. Iss. SI MAY 2002,

  35. Fang T, Valafar H., and Prestegard J., A Dipolar Coupling Based Strategy for Simultaneous Resonance Assignment and Structure Determination of Protein Backbones, Journal of the American Chemical Society; 2001, PMID:11716736

  36. Prestegard JH, Valafar H, Glushka J, Tian F, Nuclear magnetic resonance in the era of structural genomics, Biochemistry. 2001 Jul 31;40(30):8677-85, PMID:11467927

  37. Al-Hashimi HM, Valafar H, et al., Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings. J MAGN RESON 143: (2) 402-406 APR 2000, PMID:10729267

  38. H. Valafar, Valafar F et al., Predicting the effectiveness of hydroxyurea in individual sickle cell anemia patients. ARTIFINTELL MED 18: (2) 133-148 FEB 2000, PMID:10648847

  39. Valafar F, Valafar H. CCRC-Net: an Internet-based spectral database for complex carbohydrates using artificial neural networks search engines. TRAC-TREND ANAL CHEM 18: (8) 508-512 AUG 1999, Web access

  40. Cherniak R, Valafar H, et al., Cryptococcus neoformans chemotyping by quantitative analysis of H-1 nuclear magnetic resonance spectra of glucuronoxylomannans with a computer-simulated artificial neural network. CLIN DIAGN LAB IMMUN 5: (2) 146-159 MAR 1998, PMC121351, PMID:9521136

Conference and Symposium Publications

  1. Casey A. Cole, James F. Thrasher, Scott Strayer, Homayoun Valafar, Resolving Ambiguities in Accelerometer Data Due to Location of Sensor on Wrist in Application to Detection of Smoking Gesture, Contributed paper at 2017 IEEE International Conference on Biomedical and Health Informatics, February 2017, Orlando, Fl. Acceptance Rate: 38%

  2. Nicholas Boltin, Daniel Vu, Bethany Janos, Alyssa Shofner, Joan Culley, Homayoun Valafar., An AI Model for Rapid and Accurate Identification of Chemical Agents in Mass Casualty Incidents., SC INBRE Symposium (poster presentation), August 2016, Columbia, SC

  3. Hanin Omar, Casey A. Cole, Mirko Hennig, Homayoun Valafar., Characterization of Discrete State Dynamics from Residual Dipolar Couplings Using REDCRAFT., SC INBRE Symposium (poster presentation), August 2016, Columbia, SC

  4. Kenneth Nesbitt, Casey A. Cole, Nick Boltin, Yuxin Cui, Hao Ji, Min Li, Zhenhua Shang, Hanin Omar, Arjang Fahim, Misha Shtutman, Homayoun Valafar., From Zero to Gene Assembly in Three Weeks , SC INBRE Symposium (poster presentation), August 2016, Columbia, SC

  5. Devaun McFarland, Caroline Bullock, Benjamin Mueller, Homayoun Valafar., Applying MSTALI to Active Site Identification Studies. , SC INBRE Symposium (poster presentation), August 2016, Columbia, SC

  6. Arjang Fahim, Kenneth Nesbitt, Casey Cole, Homayoun Valafar., A Novel Hybrid Refinement Method Using Unassigned Residual Dipolar Couplings , SC INBRE Symposium (poster presentation), August 2016, Columbia, SC

  7. Casey Cole, Bethany Janos, Dien Anshari, Mark Macauda, Jim Thrasher, Scott Strayer, Homayoun Valafar., Detecting Smoking Gestures Using Accelerometer Data and Artificial Neural Networks , SC INBRE Symposium (poster presentation), August 2016, Columbia, SC

  8. Mary Cole Homayoun Valafar., Development of a Curriculum to Include Robotics In Middle School Classrooms And After School Clubs , SC INBRE Symposium (poster presentation), August 2016, Columbia, SC

  9. Brandon Lighten Homayoun Valafar., Protein Minimization and Its Purpose , SC INBRE Symposium (poster presentation), August 2016, Columbia, SC

  10. Nicholas Boltin, Daniel Vu, Bethany Janos, Alyssa Shofner, Joan Culley, Homayoun Valafar, An AI Model for Rapid and Accurate Identification of Chemical Agents in Mass Casualty Incidents, Proceedings of the International Conference on Health Informatics and Medical Systems (HIMS), July 2016, Las Vegas, NV. Acceptance Rate: 29%

  11. Casey A. Cole, Bethany Janos, Dien Anshari, James F. Thrasher, Scott Strayer, Homayoun Valafar, Recognition of Smoking Gesture Using Smart Watch Technology, Proceedings of the International Conference on Health Informatics and Medical Systems (HIMS), July 2016, Las Vegas, NV. Acceptance Rate: 29%

  12. Devaun McFarland, Caroline Bullock, Benjamin Mueller, Homayoun Valafar, Application of msTALI in ATPase Active Site Identification, Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP), July 2016, Las Vegas, NV. Acceptance Rate: 29%

  13. Casey A. Cole, Bethany Janos, Dien Anshari, Mark Macauda, Jim Thrasher, Scott Strayer, Homayoun Valafar, Detecting Smoking Gestures Using Accelerometer Data and Artificial Neural Networks, Oral presentation at National IDeA Symposium of Biomedical Research Excellence (NISBRE), June 2016, Washington D.C.

  14. Kenneth Nesbitt, Casey A. Cole, Nick Boltin, Yuxin Cui, Hao Ji, Min Li, Zhenhua Shang, Hanin Omar, Arjang Fahim, Misha Shtutman, Homayoun Valafar, From Zero to Gene Assembly in Three Weeks , Oral presentation at National IDeA Symposium of Biomedical Research Excellence (NISBRE), June 2016, Washington D.C.

  15. Arjang Fahim, Casey A. Cole, Homayoun Valafar, nD-PDPA: A Novel Hybrid Refinement Method Using Unassigned Residual Dipolar Couplings, 57th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Pittsburg, Pennsylvania, April 10-15, 2016

  16. Hanin Omar, Casey A. Cole, Rishi Mukhapadhyay, Mirko Hennig, Homayoun Valafar, Structure Calculation and Reconstruction of Discrete State Dynamics from Residual Dipolar Couplings using REDCRAFT, 57th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Pittsburg, Pennsylvania, April 10-15, 2016

  17. Casey A. Cole, Mirko Hennig, Homayoun Valafar, An Investigation of Minimum Data Requirement for Successful Structure Determination of Pf2048.1 with REDCRAFT, Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP), July 2015, Las Vegas, NV

  18. Hanin Omar, Casey A. Cole, Arjang Fahim, Giuliana Gusmaroli, Stephen Borgianini, Homayoun Valafar, De Novo Assembly of Uca minax Transcriptome from Next Generation Sequencing, Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP), July 2015, Las Vegas, NV

  19. Casey A. Cole, Mirko Hennig, Homayoun Valafar, Structure Elucidation of a Novel Protein from Minimal Set of Backbone RDC Data with REDCRAFT, SC INBRE Symposium (poster presentation), February 2015, Columbia, SC

  20. Casey A. Cole, Hanin Omar, Arjang Fahim, Guiliana Gusmaroli, Homayoun Valafar, Transcriptome Assembly of the Uca minax, Poster presented at National IDeA Symposium of Biomedical Research Excellence (NISBRE), June 2014, Washington D.C.

  21. Arjang Fahim, Homayoun Valafar, nDh-PDPA: n-Dimensional Hybrid Probability Density Profile Analysis, SE Regional IDeA Meeting, Nov 15-17 2013, Little Rock, AK

  22. Devaun McFarland, Homayoun Valafar, Utility of msTALI in Protein Active Site Identification, SE Regional IDeA Meeting, Nov 15-17 2013, Little Rock, AK

  23. Casey Cole, Arjang Fahim, Hanin Omar, Homayoun Valafar, Transcriptome of Uca Minax, SE Regional IDeA Meeting, Nov 15-17 2013, Little Rock, AK

  24. Ji Hao, Oliver David, Chen Mengqian, Valafar Homayoun, Shtutman Michael, Construction, selection and analysis of on-chip synthesized shRNA libraries. South Carolina INBRE Scientific Symposium, April 19-20 2013, Columbia, SC

  25. Stephanie J Irausquin and Homayoun Valafar, Quantifying the Amount of Data Required for Successful Investigations of Structure and Dynamics from Residual Dipolar Couplings, South Carolina INBRE Scientific Symposium, April 19-20 2013, Columbia, SC

  26. McFarland, D., and  Valafar, H, Utility of msTALI in Protein Active Site Identification, South Carolina INBRE Scientific Symposium, April 19-20 2013, Columbia, SC

  27. Fahim Arjang, Valafar Homayoun, A Cost Effective Method to Calculate Protein Structure, Using Unassigned NMR Data, South Carolina INBRE Scientific Symposium, April 19-20 2013, Columbia, SC

  28. Mikhail Simin, Homayoun Valafar, Protein structure determination from challenging sets of RDCs using REDCRAFT, SERMACS, 14-17 November 2012 Raleigh Convention Center, Raleigh, North Carolina

  29. Stephanie J Irausquin, Christopher Schmidt, Mikhail Simin, Homayoun Valafar, Pipeline for Residual Dipolar Coupling Analysis Allows for the Simultaneous Study of Structure and Dynamics of Challenging Proteins, SERMACS, 14-17 November 2012 Raleigh Convention Center, Raleigh, North Carolina

  30. Arjang Fahim, Mikhail Simin, Homayoun Valafar, Protein structure determination from unassigned NMR data, SERMACS, 14-17 November 2012 Raleigh Convention Center, Raleigh, North Carolina

  31. Stephanie Irausquin, Christopher Schmidt, Mikhail Simin, Homayoun Valafar, Analysis Pipeline for Simultaneous Study of Structure and Dynamics of Challenging Proteins from Residual Dipolar Couplings, 53th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Miami, Florida, April 15-20, 2012

  32. A. Fahim, M. Simin, H. Valafar, nDh-PDPA: n-Dimensional Hybrid Probability Density Profile Analysis, 53th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Miami, Florida, April 15-20, 2012

  33. Chris Schmidt, Stephanie Irausquin, and Homayoun Valafar, REDCAT Motion Prediction and Characterization, 53th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Miami, Florida, April 15-20, 2012

  34. M. Simin, P. Shealy, H. Valafar, Lowering NMR Data Requirements in Protein Structure Determination using REDCRAFT, 53th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Miami, Florida, April 15-20, 2012

  35. Fawcett, Stephanie Irausquin, Mikhail Simin, and Homayoun Valafar, An Artificial Neural Network Based Approach for Identification of Native Protein Structures using an Extended ForceField, IEEE International Conference, Bioinformatics Biomedicine, 12-15 Nov 2011 2011 (500 - 505), Atlanta, GA

  36. Stephanie Irausquin, Christopher Schmidt, Mikhail Simin, Homayoun Valafar, Study of Structure and Internal Dynamics of Challenging Proteins from Residual Dipolar Couplings, SE Regional IDeA Meeting, September 22-24, 2011, New Orleans, LA

  37. Matthew Fawcett, Stephanie Irausquin, Mikhail Simin, Homayoun Valafar, SCOPE: An Open-Source, C++ Implementation for Calculation of Protein Energetics from First Principles, International Conference on Bioinformatics Computational Biology (BIOCOMP2011), Las Vegas, July 18-21, 2011

  38. Chris Schmidt, Rishi Mukhopadhyay, and Homayoun Valafar, REDCAT Enhancements with Xplor-NIH and VMD Integration, 52th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Pacific Grove, California, April 10-15, 2011

  39. Paul Shealy, Mikhail Simin, Arjang Fahim, and Homayoun Valafar, Template-guided protein structure determination with REDCRAFT and msTALI, 52th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Pacific Grove, California, April 10-15, 2011

  40. M. Simin, P. Shealy, H. Valafar, Computational Advancements of REDCRAFT in Protein Structure Determination from RDCs, 52th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Pacific Grove, California, April 10-15, 2011

  41. Mukhopadhyay R., Simin M., Valafar H., Calculation of Protein Backbone Structure and Calculation of Trajectory of Inter-Domain Motion from Residual Dipolar Couplings, 52th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Pacific Grove, California, April 10-15, 2011

  42. Mukhopadhyay R., Simin M., Valafar H., Calculation of structure and trajectory of motion of mobile domains in proteins from residual dipolar couplings, Keystone Symposia: Frontiers of NMR in Biology, January 8 - 13, 2011 Big Sky Resort, Big Sky, Montana

  43. Mukhopadhyay R., Valafar H., Dynafold: A provably optimal algorithm for protein structure determination from N-H and C-H Residual Dipolar Couplings collected in two alignment media, 51th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Daytona Beach, Florida, April 18-23, 2010

  44. Simin M., Valafar H., Algorithmic and Methodology Improvements of REDCRAFT, 51th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Daytona Beach, Florida, April 18-23, 2010

  45. Schmidt C., Mukhopadhyay R., Valafar H., REDCAT Improvements and XplorGUI Introduction, 51th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Daytona Beach, Florida, April 18-23, 2010

  46. Mukhopadhyay R., Yandle R., Valafar H., nD-PDPA: Structural Similarity Assessment of Proteins From Unassigned Residual Dipolar Couplings, Protein Structure Initiative: 2010 NIGMS Workshop: Enabling Technologies in Structure and Function, April 19-21, 2010, Natcher Building Bethesda, Maryland

  47. Simin M., Shealy P., Valafar H., REDCRAFT: A computational Approach for Simultaneous Investigation of Structure and Dynamics of Proteins from Residual Dipolar Couplings, Protein Structure Initiative: 2010 NIGMS Workshop: Enabling Technologies in Structure and Function, April 19-21, 2010, Natcher Building Bethesda, Maryland

  48. Shealy P., Valafar H., Aligning Multiple Protein Structures using Biochemical and Biophysical Properties, International Conference on Bioinformatics and Computational Biology (BioComp09), Las Vegas July 13-16, 2009

  49. Yandle R., Mukhopadhyay R., Valafar H., Using Residual Dipolar Couplings from Two Alignment Media to Detect Structural Homology, International Conference on Bioinformatics and Computational Biology (BioComp09), Las Vegas July 13-16, 2009

  50. Simin M., Valafar H., Alternative Metric System and Data Sensitivity for Protein Structure Determination with REDCRAFT, International Conference on Bioinformatics and Computational Biology (BioComp09), Las Vegas July 13-16, 2009

  51. Mukhopadhyay R., Shealy P., Valafar H., Study of Structure and Dynamics of Proteins from Unassigned RDC Data, Keystone Symposia: Frontiers of NMR in Biology, Mew Mexico, February 15-20, 2009

  52. Shealy P., Mukhopadhyay R., Park S.H., Opella S., Valafar H., Minimum RDC Data Requirements for Protein Folding Using REDCRAFT with Angular Constraints, 50th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Monterey March 29-April 3, 2009

  53. R. Mukhopadhyay, Yandle R., H. Valafar, 2-D Probability Density Profile Analysis: Identifying Structure of an Unknown protein From Unassigned Residual Dipolar Couplings, 50th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Monterey March 29-April 3, 2009

  54. X. Miao; R. Mukhopadhyay ; H. Valafar, Estimation of order parameters and relative orientation of an unknown protein from unassigned, correlated 2D-RDC data. 49th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Monterey March 9-14

  55. P. Shealy; S. Smith; H. Valafar , Order Tensor Estimation and Assignment of Backbone Resonances Using Residual Dipolar Couplings. 49th Experimental Nuclear Magnetic Resonance Spectroscopy Conference, Monterey March 9-14

  56. E. Timko, P. Shealy, M. Bryson, and H. Valafar, Minimum Data requirements and Supplemental Angle Constraints for Protein Structure Prediction with REDCRAFT, BioComp08, Las Vegas July 14-16

  57. P. Shealy, R. Mukhopadhyay, S. Smith, H. Valafar, Automated Assignment of Backbone Resonances Using Residual Dipolar Couplings Acquired from a Protein with Known Structure, BioComp08, Las Vegas July 14-16

  58. R Mukhopadhyay, P. Shealy, H. Valafar, Protein Fold Family Recognition From Unassigned Residual Dipolar Coupling Data, BioComp08, Las Vegas July 14-16

  59. S Bansal, X. Miao, J. H. Prestegard, H. Valafar, Rapid Classification of Protein Structure Models using Unassigned NMR Data, 21st Symposium of The Protein Society, July 21, 2007, Boston, Massachusetts.

  60. S Bansal, H. Valafar, K.L. Mayer, P. LeBlond, G. Sciortino; J.H. Prestegard, Target Selection for NMR vs X-Ray Structure Determination using 1D NMR Screen, 47th ENC, April 23-28, 2006.

  61. X Miao, M. Bryson, H. Valafar, TALI: Protein Structure Alignment Using Backbone Torsion Angles. BIOCOMP 2006: 3-9

  62. M Bryson, X. Miao, H. Valafar: Process of Efficiently Parallelizing a Protein Structure Determination Algorithm. PDPTA 2006: 320-326

  63. H Valafar, Mayer K. L., LeBlond P. D., Bougault, C., Prestegard J.H., Residual Dipolar Couplings in High Throughput Backbone Solution Structure Determination of Proteins, International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS’2004). June 21-24, Las Vegas, Nevada.

  64. H Valafar, Prestegard JH, Fold Family Recognition Based on Unassigned Residual Dipolar Couplings, Computational Aspects of Biomolecular NMR, Gordon Research Conference, January 18-23, 2004, Ventura, California.

  65. H Valafar ; Prestegard JH, A New Program for RDC Analysis and Structure Validation. 44th ENC Program March 30 - April 4, 2003, Savannah, Georgia

  66. LC Morris ; Valafar H; Prestegard JH, Assignment of Backbone Resonances from Minimal NMR Data Sets Using Connectivity, Torsion Angle Constraints, and Chemical Shifts. 44th ENC Program March 30 - April 4, 2003, Savannah, Georgia

  67. KL Mayer ; Valafar H; et. al., NMR Structure Determination Using Residual Dipolar Couplings,. 44th ENC Program March 30 - April 4, 2003, Savannah, Georgia

  68. MG Ford ; Valafar H; Prestegard JH, Residual Dipolar Coupling Assisted Assignment for HSQC Based Ligand Titration Data on Galectin-1. 44th ENC Program March 30 - April 4, 2003, Savannah, Georgia

  69. RD Seidel; Juan-Carlos Amor; H Valafar; Richard A. Kahn; James H. Prestegard, Conformational Changes in human Arf1 on Nucleotide Exchange and Deletion of the N-terminal Helix using Residual Dipolar Coupling. 44th ENC Program March 30 - April 4, 2003, Savannah, Georgia

  70. K Mayer, H. Valafar, et al, NMR Structure Determination and Validation using Residual Dipolar Couplings, ISGO International Conference on Structural Genomics, Oct 10-13, 2002 Berlin

  71. K Mayer, H. Valafar, et al, The Roles of NMR in Structural Genomics at the SECSG, 43rd Experimental NMR Conference (ENC 43), April 14-19, 2002 Asilomar, CA

  72. H Valafar, Tian F., Prestegard J. H., Rapid Classification of Protein Fold Families Using a Statistical Analysis of Dipolar Couplings. 42st Experimental Nuclear Magnetic Resonance Conference (ENC 42), 2001.

  73. F Tian; Valafar H.; Prestegard J. H.; A Dipolar Coupling Based Strategy for Simultaneous Protein Resonance Assignment and Structure Determination. 42st Experimental Nuclear Magnetic Resonance Conference (ENC 42), 2001.

  74. J H. Prestegard, Tian F., H. Valafar, High Through-put NMR Analysis of Proteins at the Southeast Collaboratory for Structural Genomics. 42st Experimental Nuclear Magnetic Resonance Conference (ENC 42), 2001.

  75. H Valafar, Valafar F.; Knowledge Discovery in 1H-NMR spectra of Complex Carbohydrates using Frequency to Information Transformation (FIT). International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS’2001), p61-66.

  76. H Valafar, Valafar F., Prestegard J. H.; One and Two Dimensional Statistical Data-Mining of Protein Databank for Crystallization Patterns of Proteins. International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS’2001), p67-72.

  77. H Valafar, Tian F., Prestegard J. H., Rapid Classification of Protein Fold Families Using a Statistical Analysis of Dipolar Couplings. International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS’2001), p146-151.

  78. H Valafar, Valafar F, Reduction in the complexity of 1D 1H-NMR spectra by the use of Frequency to Information Transformation. International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS’2000), p207-212

  79. H Valafar, Muti-leveled output Neural Networks in Monosaccharide decomposition Analysis of N-linked Oligosaccharides, International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS’2000), p219-224

  80. H Valafar, Prestegard J, Data-mining of Protein Structure Databank for Crystallization patterns of Proteins. International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS’2000), p193-200

  81. H Al-Hashimi, Valafar H., et al., Resolving Orientational Ambiguities in Protein Structures Using Dipolar Couplings and Variation of Molecular Alignment, 41st Experimental Nuclear Magnetic Resonance Conference (ENC), 2000.

  82. J Glushka, Q. Teng, E. R. Zartler, Valafar H., J. Prestegard, Rapid and automated evaluation of proteins as candidates for structure determination, 41st Experimental Nuclear Magnetic Resonance Conference (ENC), 2000.

  83. Valafar, F., Valafar H. 1999. A Comparative study of Artificial Neural Networks Using Reinforcement learning and Multidimensional Bayesian Classification Using Parzen Density Estimation for Identification of GC-EIMS Spectra of Partially Methylated Alditol Acetates on the World Wide Web. International Join Conference on Artificial Intelligence International Joint Conference on Neural Networks (IJCNN 1999), Washington, DC, July 10-16, 1999

  84. Valafar, F., Valafar H. 1999. Identification of 1H-NMR Spectra of Xyloglucan Oligosaccharides: A Comparative Study of Artificial Neural Networks and Bayesian Classification Using Non-parametric Density Estimation. International Joint Conference on Neural Networks (IJCNN 1999), Washington, DC, July 10-16, 1999

  85. H Valafar, F. Valafar. 1999. Identification of 1H-NMR Spectra of N-Linked Oligosaccharides Using Artificial Neural Networks. First Joint BMES/EMBS Conference 99, p157-158.

  86. Valafar, H., F. Valafar. 1999. Prediction of a Patient's Response to a Specific Drug Treatment Using Artificial Neural Networks. First Joint BMES/EMBS Conference 99, p72-73.

  87. Valafar, H., F. Valafar and O. Ersoy. Parallel, self-organizing, consensus neural networks. International Joint Conference on Neural Network 1999 (IJCNN99).

  88. Roushanzamir, S.; Valafar, H.; Valafar, F. A comparative study of linear and quadratic discriminant classifier techniques for variable selection: a case study in predicting the effectiveness of hydroxyurea treatment of sickle cell anemia, International Joint Conference on Neural Networks, 1999 (IJCNN '99).Page(s): 3627-3631 vol.5

  89. Valafar H., F. Valafar, O. Ersoy. 1998. Parallel Implementation of Distributed Global Optimization (DGO). Proceedings of the International Conference on Parallel Distributed Processing Techniques and Applications (PDPTA'98). Volume IV, page 1782.

  90. Valafar H., F. Valafar, R. Cherniak, L. C. Morris 1998. Artificial Neural Networks in Chemotype analysis of Cryptococcus neoformans International Biomedical Engineering Days 1998 (IBED 98).

  91. Valafar H., F. Valafar, L. C. Morris, R. Cherniak 1997. Quantitative Mixture Analysis of 1H-NMR Spectra Using Artificial Neural Networks for Chemotyping of Cryptococcus neoformans. International Joint conference on Neural Networks (IJCNN '98) as part of the World Congress in Computational Intelligence (WCCI '98).

  92. Valafar H., F. Valafar, P. Albersheim, A. Darvil, A. Kutlar, K. Woods, J. Hardin. 1998. Predicting Sickle Cell Patient Response to Hydroxyurea using Artificial Neural Networks, University System of Georgia Research Symposium 1998.

  93. Cherniak R., H. Valafar, L. C. Morris, and F. Valafar 1997 Cryptococcus neoformans Chemotyping by Quantitative Analysis of 1H-NMR Spectra of Glucuronoxylomannans Using a Computer Based Neural Network. American Society for Microbiology (ASM). 97th General Meeting, Miami, Florida, May 4-8, F39 page 266.

  94. Valafar, H., F. Valafar, and O. K. Ersoy. 1996. Distributed Global Optimization (DGO). Proceedings of the International Conference on Neural Networks (IEEE-ICNN '96): 530a-536, Washington, DC, June 2-6.

  95. Cherniak R., H. Valafar, L. C. Morris, and F. Valafar 1996. Invited Talk Titled: Chemotyping of Cryptococcus Neoformans by Analysis of Glucuronoxylomannan. 3rd International Conference on Cryptococcus and Cryptococcosis. Institut Pasteur, Paris, France, September 22-26, 1996. Paper VII.1 page 129.

  96. Valafar, F., H. Valafar, O. K. Ersoy, and R. J. Schwartz. 1995. Comparative studies of two neural network architectures for modeling of human speech production. Proceedings of the International Conference on Neural Networks (IEEE-ICNN '95), Perth, Australia, November 27-December 1, Vol. 4, pp. 2056-2059.

  97. Valafar, F., H. Valafar, O. K. Ersoy, and R. J. Schwartz. 1991. Comparative Studies of Two Neural Network Architectures for Modeling of Human Speech Production. Technical Report EE91-42, Purdue University, West Lafayette, IN, October.

  98. Neural Network Architectures for Modeling of Human Speech Production. Technical Report EE91-42, Purdue University, West Lafayette, IN, October.

  99. Reddy, G.N., D.M. Elmore, H. Valafar, Design of Microprogrammed Processors Using an IBM-PC Based AHPL Simulator – a Tutorial, Summer Computer Simulation Conference (SCSC-88), Seattle, Washington, July 25-28, 1988.