Software
G. Cilingir, S.L. Broschat, and A.O.T. Lau, “ApicoAP: The first computational model for identifying apicoplast-targeted proteins in multiple species of Apicomplexa,” PLoS ONE, Vol. 7, No. 5, e36598, May 2012. doi: 10.1371/journal.pone.0036598.
G. Cilingir and S.L. Broschat, “Automated training for algorithms that learn from genomic data,” BioMed Research International, Vol. 2015, Article ID 234236, 9 pages, Jan. 2015. doi: 10.1155/2015/234236.
S. Lockwood, K.A. Brayton, J.A. Daily, and S.L. Broschat, “Whole proteome clustering of 2,307 Proteobacterial genomes reveals conserved proteins and significant annotation issues,” Frontiers in Microbiology, Vol. 10, 383, Feb. 2019. doi: 10.3389/fmicb.2019.00383.
Z. Esna Ashari, K.A. Brayton, and S.L. Broschat, “Prediction of T4SS effector proteins for Anaplasma phagocytophilum using OPT4e, a new software tool,” Frontiers in Microbiology, Vol. 10, 18 Jun. 2019. doi: 10.3389/fmicb.2019.01391.
G. de la Cruz, T. Walker, D. Herndon, K.A. Brayton, M. Ueti, and S.L. Broschat, “A sequence pattern analyzer for finding SNPs and gaps when comparing protein sequences to a pattern.”
H.N. Catanese, K.A. Brayton, and A.H. Gebremedhin, “RepeatAnalyzer: a tool for analysing and managing short-sequence repeat data,” BMC Genomics, Vol. 17, 2016. doi: 10.1186/s12864-016-2686-2.
G. Cilingir, A.O.T. Lau, and S.L. Broschat, “ApicoAMP: The first computational model for identifying apicoplast-targeted transmembrane proteins in Apicomplexa,” Journal of Microbiological Methods, Vol. 95, No. 3, pp. 313-319, Dec. 2013. doi: 10.1016/j.mimet.2013.09.017.
A. Abnousi, S.L. Broschat, and A. Kalyanaraman, “A fast alignment-free approach for de novo detection of protein conserved regions,” PLoS ONE, Vol. 11, No. 8, e0161338, Aug. 2016. doi: 10.1371/journal.pone.0161338.
A. Abnousi, S.L. Broschat, and A. Kalyanaraman, “Alignment-free clustering of large data sets of unannotated protein conserved regions using minhashing,” BMC Bioinformatics, Vol. 19, No. 1, 83, Mar. 2018. doi: 10.1186/s12859-018-2080-y.
A. Sayed Chowdhury, D.R. Call, S.L. Broschat, “PARGT: A software tool for predicting antimicrobial resistance in bacteria,” Scientific Reports, Vol. 10, No. 11033, Jul. 2020. doi: 10.1038/s41598-020-67949-9.
C. Wu, A. Kalyanaraman, and W. Cannon, “A scalable parallel algorithm for large-scale protein sequence homology detection,” Proc. International Conference on Parallel Processing (ICPP), pp. 333-342, 2010, doi: 10.1109/ICPP.2010.41.
Y. Tan and S.L. Broschat, “ccSeek: a graphical application for finding protein sequence motifs.”
D. Meng, S.L. Broschat, and D.R. Call, “A Java-based tool for the design of classification microarrays,” BMC Bioinformatics, 9:328, Aug. 2008.