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Bioinformatics and Computational Biology


Logo for ApicoAP

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.

Logo for ApicoAP Complete Suite

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.

Logo for pClust

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.

Logo for OPT4e

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.

Logo for SPA

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.”

Logo for Repeat Analyzer

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.

Logo for ApicoAMP

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.

Logo for NADDA

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.

Logo for coreClust

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.

Logo for PARGT

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.

Logo of original pClust

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.

Logo for ccSeek

Y. Tan and S.L. Broschat, “ccSeek: a graphical application for finding protein sequence motifs.”

Logo for PLASMID

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.