Selected Abstracts

  • Abstracts are typically 1-2 paragraph submissions that are reviewed and accepted predominantly as posters at conferences and workshops; some are selected to be presented as oral presentations, where indicated. Extended abstracts are typically viewed as condensed manuscript submissions of 1-3 pages, also peer-reviewed by two reviewers. All extended abstracts listed here are indexed by IEEE or ACM and links are provided. For many of the abstracts and extended abstracts listed here, actual posters presented at conferences and symposia are also provided, in pdf format.
  • Shehu's advisees indicated by: high-school (h), undergraduate (u) and graduate (g) students.
    Corresponding authors are indicated by (*).
  • A65: Amarda Shehu*.

    "Guiding Stochastic Optimization Algorithms with Experimental Data to Model Protein Energy landscapes and Structural Transitions." (abstract and presentation).

    Thematic Meeting of the Biophysical Society: Conformational Ensembles from Experimental Data and Computer Simulations.

    Berlin, Germany, August 25-29, 2017.

  • A64: Kevin Molloy, David Morrisg, and Amarda Shehu*.

    "ACM-BCB ’17 Tutorial: Robotics-inspired Algorithms for Modeling Protein Structures and Motions." (abstract and tutorial presentation, pg. 628).

    ACM BCB.

    Boston, MA, August 20-23, 2017.

  • A63: Tatiana Maximova, Wanli Qiao, Erion Plaku, Carla Mattos, Buyong Ma, Ruth Nussinov, and Amarda Shehu*.

    "From Mutations to Mechanisms and Dysfunction via Computation and Mining of Protein Energy Landscapes." (abstract and presentation).

    3DSIG at Intelligent Systems for Molecular Biology (ISMB).

    Prague, Czech Republic, July 22-23, 2017.

  • A62: Emmanuel Sapin, Kennneth A De Jong, and Amarda Shehu*.

    "Evolutionary Search For Paths on Protein Energy Landscapes." (2-page poster paper).

    ACM GECCO.

    Berlin, Germany, July 15-19, 2017.

  • A61: Amarda Shehu*.

    "Big, Molecular Structure Data Demand Automated Landscape Analysis." (abstract and presentation).

    UC Davis RTG Statistical Sciences Symposium: Geometry, Statistics, and Data Analysis.

    Davis, California, May 19-20, 2017.

  • A60: Tatiana Maximovap, Erion Plaku, and Amarda Shehu*.

    "A Sampling-based Algorithm for Modeling Protein Conformational Switching." (extdended abstract and presentation).

    3DSIG at Intelligent Systems for Molecular Biology (ISMB)

    Orlando, Florida, July 8-12, 2016. Outstanding research presentation award.

  • A59: Chris McDermott-Roe*, Katie Mitzelfelt, Maribel Marquez, Mike Grzybowski, John Bukowy, Tatiana Maximova, Amarda Shehu, Ivor Benjamin, Aron Geurts*.

    "Modeling BAG3-associated cardiomyocyte dysfunction via genome editing in induced pluripotent stem cells." (poster).

    CRISPR Precision Gene Editing Congress,

    Boston, Massachussetts, February 23-25, 2016.

  • A58: Maribel Marquez, Chris McDermott-Roe*, John Bukowy, Kurt Kolander, Judy Kuo, Tatiana Maximovap, Amarda Shehu , Ivor Benjamin, Aron Geurts*.

    "Modeling BAG3-associated cardiomyocyte dysfunction via genome editing in induced pluripotent stem cells." (poster).

    Keystone Symposia on Molecular and Cellular Biology: Heart Failure: Genetics, Genomics and Epigenetics,

    Snowbird Resort, Snowbird, Utah, April 3-7, 2016.

  • A57: Mazyar Katouzianu, Irina Hashmig, Alastair Neil, and Amarda Shehu.

    "Platform to Support Intensive Webserver Computations on Argo." (poster).

    Volgenau School of Engineering Undergraduate Research Celebration,

    Fairfax, VA, April, 2015.

  • A56: Songyue Huangu and Amarda Shehu.

    "A new Distance Function for Protein Structures for the Decoy Selection Problem in De-novo Structure Prediction." (poster).

    Volgenau School of Engineering Undergraduate Research Celebration,

    Fairfax, VA, April, 2015.

  • A55: Rudy Clauseng, Amarda Shehu, Buyong Ma, and Ruth Nussinov.

    "A Novel Evolutionary Algorithm to Model Energy Landscapes of Wildtype and Variant Sequences of H-Ras."

    Biophysical Society Meeting,

    Baltimore, MD, February, 2015.

  • A54: Rudy Clauseng, Amarda Shehu, Buyong Ma, and Ruth Nussinov.

    "Mapping the Structure Space of the Ras Protein using a Novel Hybrid Evolutionary Algorithm." (poster).

    NIH Summer Poster Day,

    Fredericks, MD, July, 2014.

  • A53: Jennifer M. Vanu, Mahmoud Namaziu, Ruxi Xiangu, Estela Blaisten-Barojas, and Amarda Shehu.

    "Structural Analysis and Dynamics of the Met-Enkephalin Peptide." (poster).

    American Chemical Society (ACS) Undergraduate Research Poster Session,

    Charlottesville, VA, April, 2014.

  • A52: Herath Pilapitiyau, Nadine Kabbani, and Amarda Shehu.

    "Modeling Binding of Amyloid beta-42 Peptide to the Alpha 7 Nicotinic Receptor." (poster)

    Presented at the Mason Annual Volgenau School of Engineering Undergraduate Research Celebration and the Mason COS Undergraduate Research Colloquium,

    Fairfax, VA, April, 2014.

  • A51: Jennifer M. Vanu, Mahmoud Namaziu, Ruxi Xiangu, Estela Blaisten-Barojas, and Amarda Shehu.

    "Conformational Sampling and Principal Component Analysis of the Met-Enkephalin Peptide." (poster)

    Presented at the Mason Annual Volgenau School of Engineering Undergraduate Research Celebration and the Mason COS Undergraduate Research Colloquium,

    Fairfax, VA, April, 2014.

  • A50: Mahmoud Namaziu, Jennifer M. Vanu, Ruxi Xiangu, Amarda Shehu, and Estela Blaisten-Barojas.

    "Molecular Dynamics Simulation of the Met-Enkephalin Peptide with Explicit Solvent." (poster)

    Presented at the Mason Annual Volgenau School of Engineering Undergraduate Research Celebration and the Mason COS Undergraduate Research Colloquium,

    Fairfax, VA, April, 2014.

  • A49: Ruxi Xiangu, Jennifer M. Vanu, Mahmoud Namaziu, Estela Blaisten-Barojas, and Amarda Shehu.

    "A Clustering Algorithm for Molecular Structures: Application on the Met-Enkephalin Peptide." (poster)

    Presented at the Mason Annual Volgenau School of Engineering Undergraduate Research Celebration and the Mason COS Undergraduate Research Colloquium,

    Fairfax, VA, April, 2014.

  • A48: Rudy Clauseng, and Amarda Shehu.

    "A PCA-guided Search Algorithm to Probe the Conformational Space of the Ras Protein." (extended abstract and poster).

    ACM Conference on Bioinf and Comp Biol (BCB),

    Washington, D.C., September, 2013.

  • A47: Irina Hashmig, and Amarda Shehu.

    "Protein-protein Docking using Information from Native Interaction Sites." (extended abstract and poster).

    ACM Conference on Bioinf and Comp Biol (BCB),

    Washington, D.C., September, 2013.

  • A46: Brian Olsong, and Amarda Shehu.

    "A Multi-objective Guided Evolutionary Search Algorithm for Sampling Near-native Protein Conformations." (poster).

    AAAI Workshop,

    Bellevenue, WA, July, 2013.

  • A45: Elena G. Randou*, Daniel Veltrig, and Amarda Shehu.

    "Towards Classification and Virtual Screening of Antimicrobial Peptides with Regression-based Binary Response Models."

    Nonclinical Biostatistics Conference (NBC),

    Villanova University, PA, 2013 (accepted as oral presentation).

  • A44: Kevin Molloyg, M. Jennifer Vanu, Daniel Barbara, and Amarda Shehu*.

    "Higher-order Representations for Automated Organization of Protein Structure Space." (poster)

    Celebration of Undergraduate Student Scholarship,

    George Mason University, Fairfax, VA, 2013.

  • A43: Sameh Salehu, Brian Olsong, and Amarda Shehu*.

    "An Evolutionary-inspired Probabilistic Search Algorithm to Structurally Characterize the Native State of a Novel Protein Sequence." (poster)

    National Council of Undergraduate Research (NCUR),

    University of Wisconsin-La Crosse, WI, 2013.

  • A42: Amarda Shehu*.

    "Probabilistic Methods for Modeling Structures and Motions of Protein Systems."

    NSF Grants Conference,

    Fairfax, VA, 2012.

  • A41: Niraja Bohidarh and Amarda Shehu*.

    "From Coarse-grained Conformations to Motion Pathways in Proteins." (poster)

    Thomas Jefferson Senior Research Day,

    Alexandria, VA, 2013.

  • A40: Bryn Reinstadler, M. Jennifer Vanu, and Amarda Shehu*.

    "Supersecondary Structure Motifs and De Novo Protein Structure Prediction." (poster)

    Grace Hopper Conference Celebration of Women in Computing.

    Baltimore, MD, 2012. [DREU Report]

  • A39: Sameh Salehu, Brian Olsong, and Amarda Shehu*.

    "An evolutionary framework to sample near-native protein conformations." (extended abstract and poster).

    CSBW at IEEE BIBM Workshops (BIBM-W), pg. 933.

    Philadelphia, PA, October 4-7, 2012. [indexed by IEEE]

  • A38: Daniel Veltrig and Amarda Shehu*.

    "Physico-chemical features for recognition of antimicrobial peptides." (extended abstract and poster).

    CSBW at IEEE BIBM Workshops (BIBM-W), pg. 942.

    Philadelphia, PA, October 4-7, 2012. [indexed by IEEE]

  • A37: Brian Olsong and Amarda Shehu*.

    "An evolutionary search framework to efficiently sample local minima in the protein conformational space." (extended abstract and poster)

    ACM BCB, pg. 590.

    Orlando, FL, September, 2012. [indexed by ACM]

  • A36: Irina Hashmig and Amarda Shehu*.

    "Sampling low-energy protein-protein configurations with basin hopping." (extended abstract and poster).

    IEEE BIBM, pg. 947.

    Philadelphia, PA, October 4-7, 2012 (best poster award). [indexed by IEEE]

  • A35: Brian Olsong and Amarda Shehu*.

    "Jumping low, jumping high: Controlling hopping in the protein energy surface." (extended abstract and poster).

    IEEE BIBM, pg. 946.

    Philadelphia, PA, October 4-7, 2012. [indexed by IEEE]

  • A34: Kevin Molloyg and Amarda Shehu*.

    "A tree-based search to bias sampling of protein decoy conformations." (extended abstract and poster).

    IEEE BIBM, pg. 978.

    Philadelphia, PA, October 4-7, 2012. [indexed by IEEE]

  • A33: Kevin Molloyg and Amarda Shehu*.

    "Mapping conformational pathways between known functional protein states." (extended abstract and poster).

    BIBMW Comput Struct Biol Workshop (CSBW), pg. 971.

    Philadelphia, PA, October 4-7, 2012. [indexed by IEEE]

  • A32: Scott Jordanh and Amarda Shehu*.

    "Refinement of Coarse-grained Near-native Protein Conformations Using AMBER FF99SB Force Field."

    Aspiring Scientist Summer Internship Program (ASSIP) Poster Presentations, (poster)

    Manassas, Virginia, August, 2012.

  • A31: Sameh Salehu, Brian Olsong, and Amarda Shehu*.

    "An Evolutionary-inspired Probabilistic Search Algorithm to Structurally Characterize the Native State of a Novel Protein Sequence." (poster)

    Celebration of Student Scholarship,

    George Mason University, Fairfax, VA, 2012.

  • A30: Sameh Salehu, Brian Olsong, and Amarda Shehu*.

    "Revisiting Evolutionary Search for Effective Sampling of Near-native Conformations in the Protein Conformational Space." (poster)

    Virginia Academy of Sciences,

    Norfolk, VA, 2012.

  • A29: Sameh Salehu and Amarda Shehu*.

    "An Evolutionary-inspired Probabilistic Search Algorithm to Structurally Characterize the Native State of a Novel Protein Sequence." (poster)

    College of Science Symposium, George Mason University,

    Fairfax, VA, 2012.

  • A28: Brian Olsong and Amarda Shehu*. "A Basin Hopping Probabilistic Search Framework to Efficiently Sample Local Minima in the Protein Conformational Space."

    Protein Society,

    San Diego, CA, 2012.

  • A27: Brian Olsong and Amarda Shehu*. "A Basin Hopping Probabilistic Search Framework to Efficiently Sample Local Minima in the Protein Conformational Space." (poster)

    Intelligent Systems for Molecular Biology (ISMB),

    Long Beach, CA, 2012.

  • A26: Kevin Molloyg and Amarda Shehu*. "Assembly of Low-Energy Protein Conformations with Heterogeneous Fragments." (extended abstract and poster).

    IEEE BIBM, pg. 991-993.

    Atlanta, GA, November 12-15, 2012. [indexed by IEEE]

  • A25: Brian S. Olsong and Amarda Shehu*. "Mapping the Protein Conformational Landscape with Adaptive Probabilistic Search." (poster).

    55th Annual Meeting of the Biophysical Society,

    Baltimore, Maryland, 2011.

  • A24: Irina Hashmig, Bahar Akbal-Delibas, Nurit Haspel, and Amarda Shehu*. "Protein Docking with Information on Evolutionary Conserved Interfaces." (poster).

    BIBMW Comput Struct Biol Workshop (CSBW),

    Atlanta, GA, November, 2011.

  • A23: Brian S. Olsong and Amarda Shehu*. "Local Minima Hopping Along the Protein Energy Surface." (poster).

    IEEE Intl Conf on Biomed and Bioinf (BIBM),

    Atlanta, GA, November, 2011.

  • A22: Sarah M. Richardson, Brian S. Olsong, Jessica S. Dymond, Randal Burns, Srinivasan Chandrasegaran, Jef D.Boeke, Amarda Shehu, and Joel S. Bader*.

    Annual RECOMB Satellite on Regulatory Genomics and Systems Biology,

    MIT, Boston, Massachusetts, 2009 (accepted as oral presentation).

  • A21: Rachael Chung, Beenish Jamilu, and Amarda Shehu*. "A Metropolis Monte Carlo Algorithm to compute Low-energy Structures of an RNA chain."

    Grace Hopper Conference Celebration of Women in Computing,

    Tucson, Arizona, 2009. [DREU Report]

  • A20: Anahita Mostaghimu, Daniel Veltrig, Amr Majulg, and Amarda Shehu*.

    Aspiring Scientist Summer Internship Program (ASSIP) Poster Presentations,

    Manassas, Virginia, 2009.

  • A19: Christopher Milesg and Amarda Shehu*.

    "Computing Symmetric HomoOligomeric Structures." (poster)

    ISMB ECCB,

    Stockholm, Sweden, 2009.

  • A18: Amarda Shehu, Lydia E. Kavraki, and Cecilia Clementi*.

    Protein Folding Dynamics Gordon Research Conference,

    Ventura, CA, 2008.

  • A17: Amarda Shehu, Lydia E. Kavraki, and Cecilia Clementi*.

    "Multiscale framework for the characterization of protein native states."

    National Meeting of the American Chemical Society,

    New Orleans, LA, 2008.

  • A16: Amarda Shehu, Lydia E. Kavraki, and Cecilia Clementi*.

    "Detailed Conformational Characterization of the Native State of Cyclic Cysteine-Rich Peptides Using Minimal Information."

    13th Annual Structural Biology Symposium at UTMB,

    Galveston, TX, May, 2007. abstract

  • A15: Amarda Shehu, Lydia E. Kavraki, and Cecilia Clementi*.

    "A Method to Model Conformational Ensembles of Proteins at Equilibrium."

    11th Annual Structural Biology Symposium at UTMB,

    Galveston, TX, May, 2006. abstract

  • A14: Amarda Shehu, Lydia E. Kavraki, and Cecilia Clementi*.

    "Advances in Predicting Protein conformational Ensembles at Equilibrium: A Multiscaling Framework."

    62nd Southwest Regional Meeting of the American Chemical Society,

    Houston, TX, October, 2006. abstract

  • A13: Amarda Shehu, Cecilia Clementi and Lydia E. Kavraki*.

    "A Computational Method for Capturing Structures and Properties in Proteins."

    23rd Annual Houston Conferenc on Biomedical Engineering Research,

    Houston, TX, February, 2006.

  • A12: Amarda Shehu, Cecilia Clementi, and Lydia E. Kavraki.

    10th Structural Biology Symposium at UTMB,

    Galveston, TX, 2005 abstract.

  • A10-11: Amarda Shehu, Cecilia Clementi, and Lydia E. Kavraki*.

    KECK Annual Research Conference of the Gulf Coast Consortia,

    Houston, TX, 2004-2005. abstract

  • A9: Amarda Shehu, Lydia E. Kavraki, and Cecilia Clementi*.

    Multiscale Modeling in Soft Matter and Biophysics Workshop,

    Institute for Pure and Applied Mathematics (IPAM) at UCLA, Los Angeles, 2005.

  • A8: Amarda Shehu, Lydia E. Kavraki, and Cecilia Clementi*.

    "Sampling Biomolecular Conformations with Spatial and Energetic Constraints."

    8th Johns Hopkins Folding Meeting,

    Baltimore, MD, March, 2005.

  • A3-7: Amarda Shehu, Cecilia Clementi, and Lydia E. Kavraki*.

    Rice University Corporate Affiliates Meeting,

    Houston, TX, 2003-2007 (best poster award in 2003).

  • A2: Amarda Shehu, M. Day, S. Good, H. Graves, C. Tamon, and C. Vanderwaart. "On Totally Shattered and Hyperuniversal Graphs."

    AMS/MAA Joint Mathematics Meeting,

    San-Diego, California, 2002 (best poster prize) [local copy].

  • A1: Amarda Shehu and Christino Tamon*.

    "Complexity Results on Testing Dimension in Graphs."

    Symposium On Undergraduate Research Experience (SURE),

    Potsdam, NY, 2001 [local copy].