Faculty Research

See our faculty research work in bioinformatics and  related  areas .

 Selected research works:

  • Wei Chen, Ali Sekmen, Barry D. Bruce, Khoa Nguyen, P. Mishra, L. Emujakporue, K. Wehbi "Computational Approaches for Predicting Interaction Sites of Cytochrome and Photosystem I", 5th International Conference on Bioinformatics and Computational Biology, March, 2013.
  • Al Nasr, K., Ranjan, D., Zubair, M., Chen, L., He, J., "Solving the Secondary Structure Matching Problem in CryoEM De Novo Modeling using a Constrained K-shortest Path Graph Algorithm", IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), accepted.
  • Al Nasr, K., Liu, C., Rwebangira, M., Burge, L., He, J., "Intensity-Based Skeletonization of CryoEM Grayscale Images Using a True Segmentation-Free Algorithm", IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). Vol. 10, No. 5, pp. 1289-1298, October 2013.
  • McKnight, A., Si, D., Al Nasr, K., Chernikov, A., Chrisochoides, N., He, J., "Estimating Loop Length from CryoEM Images at Medium Resolutions", BMC Structural Biology, 13(Suppl 1):S5, November 2013.
  • Biswas, A., Si, D., Al Nasr, K., Ranjan, D., Zubair, M., He, J., "Improved Effeciency in CryoEM Secondary Structure Topology Determination from Inaccurate Data", Journal of Bioinformatics and Computational Biology (JBCB), Vol. 10, No. 3, June 2012.
  • Si, D., Ji, S., Al Nasr, K., He, J., "A Machine Learning Approach for the Identification of Protein Secondary Structure Elements from cryoEM Density Maps", Biopolymers, Vol. 97, No. 9, September 2012, pp. 698-708.
  • Al Nasr, K., Ranjan, D., Zubair, M., He, J., "Ranking valid topologies of the Secondary Structure Elements Using A Constraint Graph", Journal of Bioinformatics and Computational Biology (JBCB), Vol. 9, No. 3, June 2011, pp. 415-430.
  • Al Nasr, K., Chen, L., He, J., “A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps”, Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), Washington DC, September 2013, pp. 479-455.
  • Wang, X.; Byers, S. Copy Number Variation in Chickens: A Review and Future Prospects. Microarrays 2014, 3, 24-38. (http://www.mdpi.com/2076-3905/3/1/24)

  • Stewart, A., Kelley, G., Kimathi, B., Subramanya, SHKV., Donker, J., Darris, C., Tyus, J., Payne, A., Byers, S., Hui, D., Nahashon, S., Chen, FC., Ivy, M. and Wang, X., 2014. Expression of potential regulatory genes in abdominal adipose tissue of broiler chickens during early development. Genetics Research International. 2014, Article ID 318304, http://www.hindawi.com/journals/gri/2014/318304/ 

  • Resnyk CW, Carré W, Wang X, Porter TE, Simon J, Le Bihan-Duval E, Duclos MJ, Aggrey SE, Cogburn LA., 2012. Transcriptional analysis of abdominal fat in genetically fat and lean chickens reveals adipokines, lipogenic genes and a link between hemostasis and leanness. BMC Genomics 16;14:557. doi: 10.1186/1471-2164-14-557 
  • M. Hayes and J. Li. "Bellerophon: a hybrid method for detecting interchromosomal rearrangements at base pair resolution using next generation sequencing data." BMC Bioinformatics 2013, 14(Suppl 5):S6 (10 April 2013). Presented at the 2013 RECOMB Workshop on Massively Parallel Sequencing (RECOMB-Seq).
  • W. Wang, X. Yin, Y-S Pyon, M. Hayes, J. Li. "Rare variant discovery and calling by sequencing pooled samples with overlaps". Bioinformatics (2013) 29(1): 29-38.
  • M. Hayes, Y.S. Pyon, J. Li (2012) A Model-Based Clustering Method for Genomic Structural Variant Prediction and Genotyping Using Paired-End Sequencing Data. PLoS ONE 7(12): e52881. doi:10.1371/journal.pone.0052881. Dec. 2012.
  • Y.S. Pyon, M. Hayes and J Li. "Model Based Clustering Approach for Identifying Structural Variation Using Next Generation Sequencing Data", Proceedings of 1st IEEE International Conference in Computational Advances in Bio and Medical Sciences (ICCABS), Feb. 2011.
  • M. Hayes and J Li. "A Linear-Time Algorithm for Analyzing Array CGH Data Using Log Ratio Triangulation", International Symposium on Bioinformatics Research and Applications (ISBRA), Lecture Notes in Bioinformatics (5542) 248-259, May 2009.
  • M. Hayes, A. Walenstein, A. Lakhotia. "Evaluation of Malware Phylogeny Modelling Systems Using Automated Variant Generation." Journal in Computer Virology, Vol. 5, No. 4, 335-343. 2009.

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