Bit Publications and Presentations

[Publications and Conference Abstracts | Online Posters and Presentations]

Publications and Conference Abstracts


Alvare, G., Roche-Lima, A. & Fristensky, B. BioLegato: a programmable, object-oriented graphic user interface. BMC Bioinformatics 24, 316 (2023). https://doi.org/10.1186/s12859-023-05436-4

Heredia-Negron, F.; Alamo-Rodriguez, N.; Oyola-Velazquez, L.; Nieves, B.; Carrasquillo, K.; Hochheiser, H.; Fristensky, B.; Daluz-Santana, I.; Fernandez-Repollet, E.; Roche-Lima, A. Evaluation of AIML + HDR—A Course to Enhance Data Science Workforce Capacity for Hispanic Biomedical Researchers. Int. J. Environ. Res. Public Health 2023, 20, 2726. https://doi.org/10.3390/ijerph20032726


Fakankun I, Fristensky B, Levin DB (2021) Genome Sequence Analysis of the Oleaginous Yeast, Rhodotorula diobovata, and Comparison of the Carotenogenic and Oleaginous Pathway Genes and Gene Products with Other Oleaginous Yeasts. J. Fungi 7:320. https://doi.org/10.3390/jof7040320
Alvare G, Roche-Lima A, Fristensky B (2020) Installing and Searching BLAST Databases in a Data Science Framework. Bioinformatics: From Algorithms to Applications Saint Petersburg, Russia, July 27-28, 2020. Poster 47

Wushke S, Spicer V, Xhang X-L, Fristensky B, Krokhin OV, Levin DB, Cicek N, Richard Sparling (2016, submitted) Genome and proteome characterization of Caldibacillus debilis GB1 core metabolism under aerobic and anaerobic conditions. BMC Genomics

Fu J, Sharma P, Spicer V, Krokhin OV, Zhang X, Fristensky B, et al. (2015) Quantitative ‘Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids. PLoS ONE 10(11): e0142322. doi:10.1371/journal.pone.0142322

Kohlmeier MG, Yudistira H, Zhang XL, Fristensky B, Levin DB, Sparling R, Oresnik IJ (2015). Draft Genome Sequence of the Bacteriocin-Producing Bradyrhizobium japonicum Strain FN1. Genome Announcements, 3(4), e00812–15. http://doi.org/10.1128/genomeA.00812-15

Fu J, Sharma P, Spicer V, Krokhin O. Zhang X-L, Fristensky B, Wilkins, John , Cicek, Nazim , Sparling, Richard , Levin, David. (2015) Effects of impurities in biodiesel-derived glycerol on growth and expression of heavy metal ion homeostasis genes and gene products in Pseudomonas putida LS46. Appl. Microbiol. and Biotech. 99:5583-5592. (doi:10. ​1007/​s00253-015-6685-z)

Roche-Lima, A., Domaratzki, M., Fristensky, B. (2014) Metabolic Network Prediction Through Pairwise Rational Kernels. BMC Bioinformatics 15:318  doi:10.1186/1471-2105-15-318

Schellenberg JJ, Verbeke TJ, McQueen P, Krokhin OV, Zhang X, Alvare G, Fristensky B, Thallinger GG, Henrissat B, Wilkins JA, Levin DB, Sparling R. (2014) Enhanced whole genome sequence and annotation of Clostridium stercorarium DSM8532T using RNA-seq transcriptomics and high-throughput proteomics. BMC Genomics. BMC Genomics 2014, 15:567  doi:10.1186/1471-2164-15-567.

Roche-Lima A, Domaratzki M, Fristensky B (2014) Pairwise Rational Kernels Obtained by Automaton Operations. pp 332-345 in Holzer M, Kutrib M (Eds.)
"Implementation and Application of Automata", Series: Lecture Notes in Computer Science,  Vol. 8587.  19 Intl. Conference, CIAA, Griessen, Germany July 30 - Aug. 2 2014. http://www.springer.com/computer/theoretical+computer+science/book/978-3-319-08845-7

Parveen K Sharma, Jilagamazhi Fu, Xiangli Zhang, Brian Fristensky, Richard Sparling and David B Levin (2014) Genome features of Pseudomonas putida LS46, a novel polyhydroxyalkanoate producer and its comparison with other P. putida strains. AMB Express  4:37  doi:10.1186/s13568-014-0037-8

Tobin J. Verbeke, Vic Spicer, Oleg V. Krokhin, Xiangli Zhang, John J. Schellenberg, Brian Fristensky, John A. Wilkins, David B. Levin, and Richard Sparling. Thermoanaerobacter thermohydrosulfuricus WC1 shows protein complement stability during the fermentation of key lignocellulose-derived substrates Appl. Environ. Microbiol. 80:1602-1615. published ahead of print 20 December 2013 , doi:10.1128/AEM.03555-13
Seminar: Fristensky B (2013) Moving targets and millions of sequencing reads - Bioinformatics lessons from an international biofuels project  Faculty of Agriculture Seminar Series, Oct. 23, 2013. (MP4 Video, 1.05 Gb, 1:06:25)
Roche-Lima, A. (2013) Metabolic Network Inference using Sequence  Kernels.  Proceedings of International Conference Intelligent Systems  for Molecular Biology and European Conference of Computational 
Biology. Berlin, Germany. July 19-20, 2013.  (http://www.iscb.org/ismbeccb2013)

Roche-Lima, A., Domaratzki, M., Fristensky, B. (2013) Supervised  Learning Methods to Infer Metabolic Network using Sequence and  Non-sequence Kernels.  Proceedings of the International Workshop Machine Learning in System Biology in Conference ISMB/ECCB'13. Berlin,  Germany. July 19-20, 2013. (http://www.iscb.org/ismbeccb2013)

Sharma PK, Fu J, Zhang X, Fristensky B, Davenport K, Chain PSG, Sparling R, Levin DB. (2013). Draft Genome Sequence of Medium Chain Length Polyhydroxyalkanoates Producing Pseudomonas putida LS46. Genome Announcements, Apr 18 1(2), e0015113.
Zhang X, Björklund NK, Tydzak T, Sparling R, Alvare G, Fristensky B (2013) The Elbow Method for Deciding Significant Fold Change Cutoffs of Differentially Experssed Genes. 17th Annual Conference on Research in Computational Molecular Biology. Bejing. April 7 - 10, 2013.

Verbeke TJ, Zhang X, Henrissat B, Spicer V, Rydzak T, Krokhin OV, Fristensky B, Levin DB, Sparling R (2013) Genomic Evaluation of Thermoanaerobacter spp. for the Construction of Designer Co-Cultures to Improve Lignocellulosic Biofuel Production. PLoS ONE 8(3): e59362. doi:10.1371/journal.pone.0059362

Alvare GGM, Roche-Lima A, Fristensky B (2012) BioPCD - A Language for GUI Development Requiring a Minimal Skill Set Int. J. Computer Appl. 57:9-16. http://www.ijcaonline.org/archives/volume57/number6/9117-3273. doi: 10.5120/9117-3273

Roche-Lima A*, Domaratzki M, Gordon N, Alvare G, Zhang J, Fristensky B (2012) Finite-State Transducer Learning Approaches Applied to Metabolic Pathways in Bacteria Poster #I5, 11th European Conference on Computational Biology, Basel, Switzerland. Sept. 9 - 12, 2012

Abiel Roche-Lima and Ruppa K Thulasiram. (2012) "Bioinformatics  algorithm based on a parallel implementation of a machine learning approach using transducers". Journal of Physics. Conference Series.  341(1).  http://iopscience.iop.org/1742-6596/341/1/012034

Roche-Lima, A., Thulasiram, R.K. (2011). A Parallel Conditional Transducer Learning Algorithm Applied to Bioinformatics. In proceeding of the International Conference HPCS 2011: High Performance Computer  in Medical Science. UQAM, Montreal, QC, Canada. June 15-17, 2011.  (http://http://2011.hpcs.ca/)

Abiel Roche-Lima and Ruppa K Thulasiram. (2011). Execution on the Westgrid of a Parallel Implementation of the Conditional Transducer Learning Algorithm Applied to Bioinformatics .HPCS 2011: High Performance Computing in Medical Science. June 15-17, 2011, Montreal, Canada. Link of the Conference site: http://2011.hpcs.ca/lang/en

Fristensky B (2007)  BIRCH: A user-oriented, locally-customizable, bioinformatics system. BMC Bioinformatics , 8:54

Online Posters and Presentations

Faculty of Agricultural and Food Sciences Seminar Series
University of Manitoba, October 23, 2013

Moving targets and millions of reads - Bioinformatics lessons from an international biofuels project  PDF, 5.8 Mb

Department of Computer Science
University of Saskatchewan, Jan. 30, 2012

BioLegato: A Programmable, Object-Oriented Graphic User Interface  PDF, 1.4 Mb

10th Annual Asia Pacific Bioinformatics Conference
Melbourne, Australia, Jan. 17 - 19, 2012

BioLegato: A Programmable, Object-Oriented Graphic User Interface  PDF, 1.4 Mb

The poster associated with this presentation won a Best Poster Award

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