Biochemistry & Molecular Biology

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  • 2020

    PEGR: A management platform for ChIP-based next generation sequencing pipelines

    Shao, D., Kellogg, G., Mahony, S., Lai, W. & Pugh, B. F., Jul 26 2020, PEARC 2020 - Practice and Experience in Advanced Research Computing 2020: Catch the Wave. Association for Computing Machinery, p. 285-292 8 p. (ACM International Conference Proceeding Series).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • 2019

    De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm

    Sahlin, K. & Medvedev, P., 2019, Research in Computational Molecular Biology - 23rd Annual International Conference, RECOMB 2019, Proceedings. Cowen, L. J. (ed.). Springer Verlag, p. 227-242 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11467 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    7 Scopus citations
  • Parallel Read Partitioning for Concurrent Assembly of Metagenomic Data

    Rengasamy, V., Kandemir, M. T., Medvedev, P. & Madduri, K., Feb 8 2019, Proceedings - 25th IEEE International Conference on High Performance Computing, HiPC 2018. Institute of Electrical and Electronics Engineers Inc., p. 324-333 10 p. 8638083. (Proceedings - 25th IEEE International Conference on High Performance Computing, HiPC 2018).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Systems biology in heterogenous tissues: Integrating multiple ∗omics datasets to understand hematopoietic differentiation

    Lichtenberg, J., Xiang, G., Heuston, E., Giardine, B., Keller, C. A., Hardison, R. C., Bodine, D. M. & Zhang, Y., Oct 2019, Proceedings - 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering, BIBE 2019. Institute of Electrical and Electronics Engineers Inc., p. 240-243 4 p. 8942000. (Proceedings - 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering, BIBE 2019).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • You wrote it, Now Get it used: Publishing your software with galaxy and bioconda

    Blankenberg, D. & Čech, M., Sep 4 2019, ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. Association for Computing Machinery, Inc, 1 p. (ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Open Access
  • 2018

    Bipartite graphs of small readability

    Chikhi, R., Jovičić, V., Kratsch, S., Medvedev, P., Milanič, M., Raskhodnikova, S. & Varma, N., 2018, Computing and Combinatorics - 24th International Conference, COCOON 2018, Proceedings. Zhu, D. & Wang, L. (eds.). Springer Verlag, p. 467-479 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10976 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Characterizing protein-DNA binding event subtypes in CHIP-exo data

    Yamada, N., Lai, W. K. M., Farrell, N., Pugh, B. F. & Mahony, S., Jan 1 2018, Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Proceedings. Raphael, B. J. (ed.). Springer Verlag, p. 291-292 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10812 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Nanoscale surface phononic crystals for characterization of complex and periodic materials using extreme ultraviolet light

    Frazer, T., Abad, B., Knobloch, J., Hernandez-Charpak, J., Cheng, H., Grede, A., Giebink, N., Mallouk, T., Mahale, P., Chen, W., Xiong, Y., Dabo, I., Crespi, V., Talreja, D., Gopalan, V., Badding, J., Kapteyn, H. & Murnane, M., Jan 1 2018, Health Monitoring of Structural and Biological Systems XII. Kundu, T. (ed.). SPIE, 106001Y. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 10600).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • 2017

    A bone-on-a-chip microdevice for long-term spontaneous 3D bone tissue formation and cancer bone metastasis

    Hao, S., Cheng, G., Wan, Y., Xia, Y., Sosnoski, D. M., Mastro, A. M. & Zheng, S. Y., Jul 26 2017, TRANSDUCERS 2017 - 19th International Conference on Solid-State Sensors, Actuators and Microsystems. Institute of Electrical and Electronics Engineers Inc., p. 2203-2206 4 p. 7994514. (TRANSDUCERS 2017 - 19th International Conference on Solid-State Sensors, Actuators and Microsystems).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Allsome sequence bloom trees

    Sun, C., Harris, R. S., Chikhi, R. & Medvedev, P., 2017, Research in Computational Molecular Biology - 21st Annual International Conference, RECOMB 2017, Proceedings. Sahinalp, S. C. (ed.). Springer Verlag, p. 272-286 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10229 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    13 Scopus citations
  • Statistical Compression of Protein Folding Patterns for Inference of Recurrent Substructural Themes

    Subramanian, R., Allison, L., Stuckey, P. J., Banda, M. G. D. L., Abramson, D., Lesk, A. M. & Konagurthu, A. S., May 8 2017, Proceedings - DCC 2017, 2017 Data Compression Conference. Bilgin, A., Serra-Sagrista, J., Marcellin, M. W. & Storer, J. A. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 340-349 10 p. 7923707. (Data Compression Conference Proceedings; vol. Part F127767).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    5 Scopus citations
  • 2016

    Concentrating membrane proteins without concentrating detergent using ultrafiltration

    Feroz, H., Vandervelden, C., Ikwuagwu, B., Ferlez, B., Baker, C. S., Grzelakowski, M., Golbeck, J. H., Zydney, A. L. & Kumar, M., Jan 1 2016, 26th Annual Meeting of the North American Membrane Society, NAMS 2016. North American Membrane Society, p. 207-208 2 p. (26th Annual Meeting of the North American Membrane Society, NAMS 2016).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Fidelity of Nucleotide Incorporation by the RNA-Dependent RNA Polymerase from Poliovirus

    Cameron, C. E., Moustafa, I. M. & Arnold, J. J., 2016, DNA Replication Across Taxa, 2016. Kaguni, L. S. & Oliveira, M. T. (eds.). Academic Press, p. 293-323 31 p. (Enzymes; vol. 39).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    11 Scopus citations
  • Utrafiltration to concentrate membrane proteins without concentrating detergents

    Feroz, H., Vandervelden, C., Ikwuagwu, B., Ferlez, B., Baker, C. S., Grzelakowski, M., Golbeck, J. H., Zydney, A. L. & Kumar, M., Jan 1 2016, 26th Annual Meeting of the North American Membrane Society, NAMS 2016. North American Membrane Society, p. 215-216 2 p. (26th Annual Meeting of the North American Membrane Society, NAMS 2016).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • 2015

    Galaxy cluster to cloud-Genomics at scale

    The Galaxy Team, Jan 23 2015, Proceedings of GCE 2014: 9th Gateway Computing Environments Workshop, held in conjunction with SC 2014: The International Conference for High Performance Computing, Networking, Storage and Analysis. Institute of Electrical and Electronics Engineers Inc., p. 47-50 4 p. 7021850. (Proceedings of GCE 2014: 9th Gateway Computing Environments Workshop, held in conjunction with SC 2014: The International Conference for High Performance Computing, Networking, Storage and Analysis).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    4 Scopus citations
  • 2014

    An integrated analysis of genome-wide DNA Methylation and genetic variants underlying etoposide-induced cytotoxicity in European and African populations

    Li, R., Kim, D., Dudek, S. M. & Ritchie, M. D., Jan 1 2014, Applications of Evolutionary Computation - 17th European Conference, EvoApplications 2014, Revised Selected Papers. Esparcia-Alcázar, A. I. (ed.). Springer Verlag, p. 928-938 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8602).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding

    Mahony, S., Edwards, M. D., Mazzoni, E. O., Sherwood, R. I., Kakumanu, A., Morrison, C. A., Wichterle, H. & Gifford, D. K., 2014, Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Proceedings. Springer Verlag, p. 175-176 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8394 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Benefits of accurate imputations in GWAS

    Verma, S. S., Peissig, P., Cross, D., Waudby, C., Brilliant, M., McCarty, C. A. & Ritchie, M. D., Jan 1 2014, Applications of Evolutionary Computation - 17th European Conference, EvoApplications 2014, Revised Selected Papers. Esparcia-Alcázar, A. I. (ed.). Springer Verlag, p. 877-889 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8602).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Dissecting the obesity disease landscape: Identifying gene-gene interactions that are highly associated with body mass index

    De, R., Holmes, M. V., Moore, J. H., Ritchie, M. D., Verma, S. S., Asselbergs, F. W., Keating, B. J. & Gilbert-Diamond, D., Dec 17 2014, International Conference on Systems Biology, ISB. Wu, L-Y., Wang, Y., Chen, L. & Zhang, X-S. (eds.). IEEE Computer Society, p. 124-131 8 p. 6990744

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Excitation of multiple surface-plasmon-polariton waves and waveguide modes in a 1D photonic crystal atop a 2D metal grating

    Liu, L., Faryad, M., Hall, A. S., Barber, G. D., Erten, S., Mallouk, T. E., Lakhtakia, A. & Mayer, T. S., 2014, Nonimaging Optics: Efficient Design for Illumination and Solar Concentration XI. Winston, R. & Gordon, J. M. (eds.). SPIE, 919104. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 9191).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Microfluidic cell co-culture using standing surface acoustic wave (SSAW)

    Li, S., Guo, F., Chen, Y., Ding, X., Li, P., Cameron, C. E. & Huang, T. J., Jan 1 2014, 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014. Chemical and Biological Microsystems Society, p. 533-535 3 p. (18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • On sufficient statistics of least-squares superposition of vector sets

    Konagurthu, A. S., Kasarapu, P., Allison, L., Collier, J. H. & Lesk, A. M., 2014, Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Proceedings. Springer Verlag, p. 144-159 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8394 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    5 Scopus citations
  • Optimization of a spectrum splitter using differential evolution algorithm for solar cell applications

    Fan, L., Faryad, M., Barber, G. D., Mallouk, T. E., Monk, P. B. & Lakhtakia, A., Jan 1 2014, Nonimaging Optics: Efficient Design for Illumination and Solar Concentration XI. Winston, R. & Gordon, J. M. (eds.). SPIE, 91910I. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 9191).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Replication of SCN5A associations with electrocardiographic traits in African Americans from clinical and epidemiologic studies

    Jeff, J. M., Brown-Gentry, K., Goodloe, R., Ritchie, M. D., Denny, J. C., Kho, A. N., Armstrong, L. L., McClellan, B., Mayo, P., Allen, M., Jin, H., Gillani, N. B., Schnetz-Boutaud, N., Dilks, H. H., Basford, M. A., Pacheco, J. A., Jarvik, G. P., Chisholm, R. L., Roden, D. M., Geoffrey Haye, M. & 1 others, Crawford, D. C., 2014, Applications of Evolutionary Computation - 17th European Conference, EvoApplications 2014, Revised Selected Papers. Esparcia-Alcázar, A. I. (ed.). Springer Verlag, p. 939-951 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8602).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • 2013

    A graph-based integration of multimodal brain imaging data for the detection of early mild cognitive impairment (E-MCI)

    Kim, D., Kim, S., Risacher, S. L., Shen, L., Ritchie, M. D., Weiner, M. W., Saykin, A. J. & Nho, K., 2013, Multimodal Brain Image Analysis - Third International Workshop, MBIA 2013, Held in Conjunction with MICCAI 2013, Proceedings. p. 159-169 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8159 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    9 Scopus citations
  • A sustainable national gateway for biological computation

    Taylor, J., Ropelewski, A., Zhang, Z., Nekrutenko, A., Palencia, J., Sanielevici, S., Coraor, N., Yanovich, J., Blood, P. D. & Budden, R., 2013, Proceedings of the XSEDE 2013 Conference: Gateway to Discovery. 32. (ACM International Conference Proceeding Series).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • CARS holography

    Edwards, P. S., Shi, K., Hu, J., Xu, Q., Wang, Y., Psaltis, D. & Liu, Z., Dec 1 2013, 2013 IEEE Photonics Conference, IPC 2013. p. 372-373 2 p. 6656592

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Effect of grating period on the excitation of multiple surface-plasmon- polariton waves guided by the interface of a metal grating and a photonic crystal

    Hall, A. S., Faryad, M., Barber, G. D., Lakhtakia, A. & Mallouk, T. E., Jun 10 2013, Physics, Simulation, and Photonic Engineering of Photovoltaic Devices II. 862003. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 8620).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    3 Scopus citations
  • Novel format chromatographic columns for improved overall analytical performance

    Gaddes, D. E., Westland, J. L., Dorman, F. L. & Tadigadapa, S., Dec 1 2013, 2013 Transducers and Eurosensors XXVII: The 17th International Conference on Solid-State Sensors, Actuators and Microsystems, TRANSDUCERS and EUROSENSORS 2013. p. 238-241 4 p. 6626746. (2013 Transducers and Eurosensors XXVII: The 17th International Conference on Solid-State Sensors, Actuators and Microsystems, TRANSDUCERS and EUROSENSORS 2013).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Pretreatment of refractory gold ores using cell-free extracts of P. chrysosporium: A preliminary study

    Ofori-Sarpong, G., Osseo-Asare, K. & Tien, M., 2013, Integration of Scientific and Industrial Knowledge on Biohydrometallurgy. p. 427-430 4 p. (Advanced Materials Research; vol. 825).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    3 Scopus citations
  • Tunable standing surface acoustic wave (SSAW)-based multichannel droplet sorter

    Li, S., Ding, X., Guo, F., Chen, Y., Cameron, C. E. & Huang, T. J., Jan 1 2013, 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013. Chemical and Biological Microsystems Society, p. 311-313 3 p. (17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013; vol. 1).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • 2012

    A biologically informed method for detecting associations with rare variants

    Buchanan, C. C., Wallace, J. R., Frase, A. T., Torstenson, E. S., Pendergrass, S. A. & Ritchie, M. D., 2012, Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 10th European Conference, EvoBIO 2012, Proceedings. p. 201-210 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7246 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Comparison of methods for meta-dimensional data analysis using in silico and biological data sets

    Holzinger, E. R., Dudek, S. M., Frase, A. T., Fridley, B., Chalise, P. & Ritchie, M. D., 2012, Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 10th European Conference, EvoBIO 2012, Proceedings. p. 134-143 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7246 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    9 Scopus citations
  • Lessons learned from Galaxy, a web-based platform for high-throughput genomic analyses

    Goecks, J., Afgan, E., Baker, D., Blankenberg, D., Coraor, N., Eberhard, C., Von Kuster, G., Lazarus, R., Li, K., McManus, S., Nekrutenko, A. & Taylor, J., Dec 1 2012, 2012 IEEE 8th International Conference on E-Science, e-Science 2012. 6404442. (2012 IEEE 8th International Conference on E-Science, e-Science 2012).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    4 Scopus citations
  • 2011

    ATHENA optimization: The effect of initial parameter settings across different genetic models

    Holzinger, E. R., Dudek, S. M., Torstenson, E. C. & Ritchie, M. D., May 13 2011, Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 9th European Conference, EvoBIO 2011, Proceedings. p. 48-58 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6623 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    5 Scopus citations
  • Coherent anti-Stokes Raman scattering (CARS) holographic biological imaging

    Edwards, P. S., Shi, K., Hu, J., Xu, Q., Wang, Y., Psaltis, D. & Liu, Z., Dec 1 2011, CLEO: Science and Innovations, CLEO_SI 2011.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Coherent anti-Stokes Raman scattering (CARS) holographic biological imaging

    Edwards, P. S., Shi, K., Hu, J., Xu, Q., Wang, Y., Psaltis, D. & Liu, Z., Jan 1 2011, 2011 Conference on Lasers and Electro-Optics: Laser Science to Photonic Applications, CLEO 2011. IEEE Computer Society, 5950424. (2011 Conference on Lasers and Electro-Optics: Laser Science to Photonic Applications, CLEO 2011).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers

    Medvedev, P., Pham, S., Chaisson, M., Tesler, G. & Pevzner, P., 2011, Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. Bafna, V. & Sahinalp, S. C. (eds.). Springer Verlag, p. 238-251 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6577 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    14 Scopus citations
  • Parametric study of micropillar array solar cells

    Yoon, H. P., Yuwen, Y. A., Shen, H., Podraza, N. J., Mallouk, T. E., Dickey, E. C., Redwing, J. M., Wronski, C. R. & Mayer, T. S., Dec 1 2011, Program - 37th IEEE Photovoltaic Specialists Conference, PVSC 2011. p. 303-306 4 p. 6185905. (Conference Record of the IEEE Photovoltaic Specialists Conference).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    7 Scopus citations
  • Shortest paths between shortest paths and independent sets

    Kamiński, M., Medvedev, P. & Milanič, M., 2011, Combinatorial Algorithms - 21st International Workshop, IWOCA 2010, Revised Selected Papers. p. 56-67 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6460 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    10 Scopus citations
  • Use of biological knowledge to inform the analysis of gene-gene interactions involved in modulating virologic failure with efavirenz-containing treatment regimens in art-naïve ACTG clinical trials participants

    Grady, B. J., Torstenson, E. S., McLaren, P. J., De Bakker, P. I. W., Haas, D. W., Robbins, G. K., Gulick, R. M., Haubrich, R., Ribaudo, H. & Ritchie, M. D., 2011, Pacific Symposium on Biocomputing 2011, PSB 2011. p. 253-264 12 p. (Pacific Symposium on Biocomputing 2011, PSB 2011).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    19 Scopus citations
  • Visual integration of results from a large DNA biobank (BIOVU) using synthesis-view

    Pendergrass, S., Dudek, S. M., Roden, D. M., Crawford, D. C. & Ritchie, M. D., 2011, Pacific Symposium on Biocomputing 2011, PSB 2011. p. 265-275 11 p. (Pacific Symposium on Biocomputing 2011, PSB 2011).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    13 Scopus citations
  • 2010

    Finding unique filter sets in plato: A precursor to efficient interaction analysis in gwas data

    Grady, B. J., Torstenson, E., Dudek, S. M., Giles, J., Sexton, D. & Ritchie, M. D., 2010, Pacific Symposium on Biocomputing 2010, PSB 2010. p. 315-326 12 p. (Pacific Symposium on Biocomputing 2010, PSB 2010).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    48 Scopus citations
  • Grammatical evolution of neural networks for discovering epistasis among quantitative trait loci

    Turner, S. D., Dudek, S. M. & Ritchie, M. D., 2010, Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 8th European Conference, EvoBIO 2010, Proceedings. Springer Verlag, p. 86-97 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6023 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    18 Scopus citations
  • Incorporating domain knowledge into evolutionary computing for discovering gene-gene interaction

    Turner, S. D., Dudek, S. M. & Ritchie, M. D., Nov 12 2010, Parallel Problem Solving from Nature, PPSN XI - 11th International Conference, Proceedings. PART 1 ed. p. 394-403 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6238 LNCS, no. PART 1).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Initialization parameter sweep in ATHENA: Optimizing neural networks for detecting gene-gene interactions in the presence of small main effects

    Holzinger, E. R., Buchanan, C. C., Dudek, S. M., Torstenson, E. C., Turner, S. D. & Ritchie, M. D., 2010, Proceedings of the 12th Annual Genetic and Evolutionary Computation Conference, GECCO '10. p. 203-210 8 p. (Proceedings of the 12th Annual Genetic and Evolutionary Computation Conference, GECCO '10).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    15 Scopus citations
  • Screening for cellulose nanowhiskers binding peptides by phage display

    Guo, J., Catchmark, J. M., Tien, M. & Kao, T. H., 2010, American Society of Agricultural and Biological Engineers Annual International Meeting 2010, ASABE 2010. American Society of Agricultural and Biological Engineers, p. 5137-5149 13 p. (American Society of Agricultural and Biological Engineers Annual International Meeting 2010, ASABE 2010; vol. 6).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • 2009

    Aligning two genomic sequences that contain duplications

    Hou, M., Riemer, C., Berman, P., Hardison, R. C. & Miller, W., Dec 1 2009, Comparative Genomics - International Workshop, RECOMB-CG 2009, Proceedings. p. 98-110 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5817 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Biofilter: A knowledge-integration system for the multi-locus analysis of genome-wide association studies

    Bush, W. S., Dudek, S. M. & Ritchie, M. D., 2009, Pacific Symposium on Biocomputing 2009, PSB 2009. p. 368-379 12 p. (Pacific Symposium on Biocomputing 2009, PSB 2009).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    108 Scopus citations
  • Biosynthesis of cellulose binding domains (CBDs)

    Guo, J., Tien, M. & Catchmark, J. M., 2009, American Society of Agricultural and Biological Engineers Annual International Meeting 2009, ASABE 2009. p. 5075-5087 13 p. (American Society of Agricultural and Biological Engineers Annual International Meeting 2009, ASABE 2009; vol. 8).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution