Biochemistry & Molecular Biology

  • United States

Research Output 1961 2019

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Conference contribution
2019

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

Sahlin, K. & Medvedev, P., Jan 1 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

Clustering
Nanopore
Nanopores
Breadth
Reconstruction Algorithm

Parallel Read Partitioning for Concurrent Assembly of Metagenomic Data

Rengasamy, V., Kandemir, M., 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

Concurrent
Partitioning
Soils
Minimizer
Data storage equipment
2018
1 Citation (Scopus)

Bipartite graphs of small readability

Chikhi, R., Jovičić, V., Kratsch, S., Medvedev, P., Milanič, M., Raskhodnikova, S. & Varma, N., Jan 1 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

Bioinformatics
Bipartite Graph
Chain Graph
Graph in graph theory
Polynomials

Characterizing protein-DNA binding event subtypes in CHIP-exo data

Yamada, N., Lai, W., Farrell, N., Pugh, B. F. & Mahony, S. A., Jan 1 2018, Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Proceedings. 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

DNA-binding Protein
DNA
Proteins

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. C., Mallouk, T. E., Mahale, P., Chen, W., Xiong, Y., Dabo, I., Crespi, V. H., Talreja, D., Gopalan, V., Badding, J. V., 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

crystal surfaces
Ultraviolet
ultraviolet radiation
Extremes
Crystal
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., 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

metastasis
bones
Bone
cancer
chips
1 Citation (Scopus)

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. & 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

Protein folding
Glossaries
Proteins
HTML
Websites
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. & 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

Detergents
Ultrafiltration
Proteins
Membranes
4 Citations (Scopus)

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

Cameron, C. E., Moustafa, I. & Arnold, J. J., Jan 1 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

RNA Replicase
Poliovirus
Nucleotides
Viruses
Antiviral Agents

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. & 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

Detergents
Proteins
Membranes
2015
4 Citations (Scopus)

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

Galaxies
Genomics
2014
1 Citation (Scopus)

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

Cytotoxicity
Methylation
Genome
Genes
Drugs
1 Citation (Scopus)

An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding

Mahony, S. A., Edwards, M. D., Mazzoni, E. O., Sherwood, R. I., Kakumanu, A., Morrison, C. A., Wichterle, H. & Gifford, D. K., Jan 1 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

Integrated Model
Chip
1 Citation (Scopus)

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

Imputation
Genes
Association reactions
Quality control
Assays
1 Citation (Scopus)

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

Obesity
Nucleotides
Polymorphism
Single nucleotide Polymorphism
Multifactor Dimensionality Reduction

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., Erten, S., Mallouk, T. E., Lakhtakia, A. & Mayer, T. S., Jan 1 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

Surface Plasmon Polariton
Photonic crystals
Photonic Crystal
polaritons
Gratings

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

Microfluidics
Surface waves
Acoustic waves
Biocompatibility
Acoustics
5 Citations (Scopus)

On sufficient statistics of least-squares superposition of vector sets

Konagurthu, A. S., Kasarapu, P., Allison, L., Collier, J. H. & Lesk, A., 2014, Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Proceedings. Springer Verlag, Vol. 8394 LNBI. 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

Set of vectors
Sufficient Statistics
Superposition
Least Squares
Statistics

Optimization of a spectrum splitter using differential evolution algorithm for solar cell applications

Fan, L., Faryad, M., Barber, G., Mallouk, T. E., Monk, P. B. & Lakhtakia, A., 2014, Nonimaging Optics: Efficient Design for Illumination and Solar Concentration XI. SPIE, Vol. 9191. 91910I

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

Differential Evolution Algorithm
Solar Cells
Gratings
Solar cells
solar cells

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., Jan 1 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

Electronic medical equipment
Replication
Nutrition
Electrocardiography
Metaanalysis
2013
6 Citations (Scopus)

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., Sep 5 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

Alzheimer's Disease
Brain
Imaging
Imaging techniques
Graph in graph theory

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., Aug 26 2013, Proceedings of the XSEDE 2013 Conference: Gateway to Discovery. 32

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

Galaxies
Job analysis
Websites
Servers
Data storage equipment

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

Holography
holography
Imaging techniques
imaging techniques
Labels
3 Citations (Scopus)

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., Lakhtakia, A. & Mallouk, T. E., Jun 10 2013, Physics, Simulation, and Photonic Engineering of Photovoltaic Devices II. Vol. 8620. 862003

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

Surface Plasmon Polariton
Guided Waves
Guided electromagnetic wave propagation
Photonic crystals
Photonic Crystal

Novel format chromatographic columns for improved overall analytical performance

Gaddes, D. E., Westland, J. L., Dorman, Jr., F. L. & Tadigadapa, S. A., 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

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

Tubing
Gas chromatography
High temperature operations
Microfabrication
Tailings
1 Citation (Scopus)

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

Ofori-Sarpong, G., Osseo-Asare, K. A. & Tien, M., Nov 6 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

Refractory materials
Ores
Gold
Fungi
Sulfur

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

Surface waves
Acoustic waves
Oils
Acoustics
Water
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., Apr 3 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

Genes
Binning
Genome
Gene
Collapsing
8 Citations (Scopus)

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., Apr 3 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

Gene expression
Data analysis
Gene Expression
Genotype
Cytotoxicity
4 Citations (Scopus)

Lessons learned from Galaxy, a web-based platform for high-throughput genomic analyses

Goecks, J., Afgan, E., Baker, D., Blankenberg, D. J., 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

Throughput
Software engineering
Assays
Visualization
Genomics
2011
5 Citations (Scopus)

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

Genes
Optimization
Genome
Grammatical Evolution
Gene

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

holography
Raman scattering
selectivity
Raman spectra
Imaging techniques

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

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

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

holography
Raman scattering
selectivity
Raman spectra
Imaging techniques
12 Citations (Scopus)

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., Apr 4 2011, Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. 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

De Bruijn Graph
Genome
Genes
Post-processing
Graph in graph theory
4 Citations (Scopus)

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

Solar cell arrays
Aspect ratio
Solar cells
Doping (additives)
Gases
9 Citations (Scopus)

Shortest paths between shortest paths and independent sets

Kamiński, M., Medvedev, P. & Milanič, M., Apr 4 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

Reconfiguration
Independent Set
Shortest path
Polynomials
Graph in graph theory
16 Citations (Scopus)

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., Dec 1 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

efavirenz
Art
Acquired Immunodeficiency Syndrome
Genes
Clinical Trials
12 Citations (Scopus)

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., Dec 1 2011, Pacific Symposium on Biocomputing 2011, PSB 2011. p. 265-275 11 p.

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

Single Nucleotide Polymorphism
DNA
Electronic Health Records
Nucleic Acid Databases
Crohn Disease
2010
43 Citations (Scopus)

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., Dec 1 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

Genes
Statistics
Genome-Wide Association Study
Genetic Models
Single Nucleotide Polymorphism
18 Citations (Scopus)

Grammatical evolution of neural networks for discovering epistasis among quantitative trait loci

Turner, S. D., Dudek, S. M. & Ritchie, M. D., May 20 2010, Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 8th European Conference, EvoBIO 2010, Proceedings. 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

Grammatical Evolution
Epistasis
Quantitative Trait Loci
Genes
Neural Networks

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

Evolutionary Computing
Domain Knowledge
Genes
Gene
Interaction
14 Citations (Scopus)

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., Aug 27 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

Main Effect
Sweep
Initialization
Genes
Neural Networks

Screening for cellulose nanowhiskers binding peptides by phage display

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

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

Cellulose
bacteriophages
Bacteriophages
cellulose
peptides
2009
1 Citation (Scopus)

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

Duplication
Genomics
Alignment
Speciation
Mouse
99 Citations (Scopus)

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

Bush, W. S., Dudek, S. M. & Ritchie, M. D., Dec 1 2009, Pacific Symposium on Biocomputing 2009, PSB 2009. p. 368-379 12 p.

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

Systems Integration
Biofilters
Genome-Wide Association Study
Genes
Information Storage and Retrieval

Biosynthesis of cellulose binding domains (CBDs)

Guo, J., Tien, M. & Catchmark, J. M., Dec 1 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

Cellulose
cellulose
biosynthesis
cellulose 1,4-beta-cellobiosidase
Cellulose 1,4-beta-Cellobiosidase

Cerium zirconium lanthanum dioxide catalyst supports impregnated with platinum/palladium for the methanol steam reforming reaction

Supalo, C. A. & Mallouk, T. E., Dec 1 2009, American Chemical Society - 237th National Meeting and Exposition, ACS 2009, Abstracts of Scientific Papers. (ACS National Meeting Book of Abstracts).

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

Cerium
Lanthanum
Steam reforming
Palladium
Reforming reactions
6 Citations (Scopus)

Conquering the needle-in-a-haystack: How correlated input variables beneficially alter the fitness landscape for neural networks

Turner, S. D., Ritchie, M. D. & Bush, W. S., Jul 23 2009, Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 7th European Conference, EvoBIO 2009, Proceedings. p. 80-91 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5483 LNCS).

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

Fitness Landscape
Variable Selection
Evolutionary algorithms
Neural Networks
Neural networks

Genetic variation detection using maximum likelihood estimator

Alqallaf, A. K., Tewfik, A. H. & Selleck, S. B., Oct 2 2009, 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009. 5174365

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

Maximum likelihood
DNA
Comparative Genomic Hybridization
Disease Susceptibility
Medical Genetics
1 Citation (Scopus)

Identifying patterns of copy number variants in casecontrol studies of human genetic disorders

Alqallafl, A. K., Tewfik, A. H., Krakowiak, P., Tassone, F., Davis, R., Hansen, R., Hertz-Picciotto, I., Pessah, I., Gregg, J. & Selleck, S. B., Oct 2 2009, 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009. 5174366. (2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009).

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

DNA Copy Number Variations
Inborn Genetic Diseases
Medical Genetics
DNA
Oligonucleotides