selected publications
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academic article
- Shell Disorder Models Detect That Omicron Has Harder Shells with Attenuation but Is Not a Descendant of the Wuhan-Hu-1 SARS-CoV-2. Biomolecules. 12. 2022
- Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere Methylobacterium Diversity. MBio. 13. 2022
- Variation in Human Milk Composition Is Related to Differences in Milk and Infant Fecal Microbial Communities. Microorganisms. 9:1153. 2021
- Key genetic variants associated with variation of milk oligosaccharides from diverse human populations. Genomics. 113:1867-1875. 2021
- Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome. Frontiers in Cellular and Infection Microbiology. 11:622550. 2021
- Multipathogen Analysis of IgA and IgG Antigen Specificity for Selected Pathogens in Milk Produced by Women From Diverse Geographical Regions: The INSPIRE Study. Frontiers in Immunology. 11:614372. 2021
- A Novel Strategy for the Development of Vaccines for SARS-CoV-2 (COVID-19) and Other Viruses Using AI and Viral Shell Disorder. Journal of Proteome Research. 19:4355-4363. 2020
- The Skin Microbiome Facilitates Adaptive Tetrodotoxin Production in Poisonous Newts. eLife. 9. 2020
- Shell Disorder Analysis Predicts Greater Resilience of the SARS-CoV-2 (COVID-19) Outside the Body and in Body Fluids. Microbial Pathogenesis. 104177. 2020
- What's Normal? Microbiomes in Human Milk and Infant Feces Are Related to Each Other but Vary Geographically: The INSPIRE Study. Frontiers in Nutrition. 7. 2020
- Rigidity of the Outer Shell Predicted by a Protein Intrinsic Disorder Model Sheds Light on the COVID-19 (Wuhan-2019-nCoV) Infectivity. Biomolecules. 10:331. 2020
- Nipah shell disorder, modes of infection, and virulence. Microbial Pathogenesis. 141:103976. 2020
- Shell Disorder Analysis Suggests That Pangolins Offered a Window for a Silent Spread of an Attenuated SARS-CoV-2 Precursor among Humans.. Journal of Proteome Research. 2020
- Shell disorder analysis predicts greater resilience of the SARS-CoV-2 (COVID-19) outside the body and in body fluids.. Microbial Pathogenesis. 144:104177. 2020
- HIV Vaccine Mystery and Viral Shell Disorder.. Biomolecules. 9:178. 2019
- Household Composition and the Infant Fecal Microbiome: The INSPIRE Study. American Journal of Physical Anthropology. 169:526-539. 2019
- Zika and Flavivirus Shell Disorder: Virulence and Fetal Morbidity. Biomolecules. 9:710. 2019
- New NSF policy will stifle innovation. Science (New York, N.Y). 362:297-298. 2018
- What's Normal? Immune Profiling of Human Milk from Healthy Women Living in Different Geographical and Socioeconomic Settings. Frontiers in Immunology. 8.0. 2017
- What's normal? Oligosaccharide concentrations and profiles in milk produced by healthy women vary geographically. American Journal of Clinical Nutrition. 105.0:1086.0-1100.0. 2017
- Defining and simulating open-ended novelty: requirements, guidelines, and challenges. Theory in Biosciences. 135:131-161. 2016
- Seed: a user-friendly tool for exploring and visualizing microbial community data. Bioinformatics. 31:602-603. 2015
- Network analysis suggests a potentially 'evil' alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities. Scientific Reports. 5. 2015
- Machine learning classifiers provide insight into the relationship between microbial communities and bacterial vaginosis. Biodata Mining. 8. 2015
- MetAmp: combining amplicon data from multiple markers for OTU analysis. Bioinformatics. 31:1830-1832. 2015
- Machine learning techniques accurately classify microbial communities by bacterial vaginosis characteristics. PLOS One. 9:e87830. 2014
- Estimation of viral species richness from shotgun metagenomes using a frequency count approach. Microbiome. 1. 2013
- Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life. Briefings in Bioinformatics. 13:420-429. 2013
- Microbiome studies: analytical tools and techniques. Pacific Symposium on Biocomputing. 2013
- mcaGUI: microbial community analysis R-Graphical User Interface (GUI). Bioinformatics. 28. 2013
- Introduction to special section: Best of EuroGP/EvoBIO. Genetic Programming and Evolvable Machines. 14:429-430. 2013
- SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching. Journal of Data Mining in Genomics and Proteomics. 4:1-6. 2013
- Serial Analysis of the Gut and Respiratory Microbiome in Cystic Fibrosis in Infancy: Interaction between Intestinal and Respiratory Tracts and Impact of Nutritional Exposures. MBio. 3:e00251. 2012
- Estimating population diversity with CatchAll. Bioinformatics. 28:1045-1047. 2012
- Estimating population diversity with unreliable low frequency counts. Pacific Symposium on Biocomputing. 203-212. 2012
- Gut microbial colonisation in premature neonates predicts neonatal sepsis. Archives of Disease in Childhood. 97:F456-F462. 2012
- Characterization of the diversity and temporal stability of bacterial communities in human milk. PLOS One. 6:e21313. 2011
- Microbial Communities as Experimental Units.. BioScience. 61. 2011
- Microbiome studies: psb 2011 special session introduction.. Pacific Symposium on Biocomputing. . 2011
- OTUbase: an R infrastructure package for operational taxonomic unit data.. Bioinformatics. 27. 2011
- Computing with bacterial constituents, cells and populations: from bioputing to bactoputing. Theory in Biosciences. 130:211-228. 2011
- Bacterial diversity in a glacier foreland of the high Arctic.. Molecular Ecology. 19 Suppl 1. 2010
- The human milk microbiome: a potential influence on mammary health and bacterial colonization of the infant gut. FASEB Journal. 24. 2010
- Application of ecological network theory to the human microbiome.. Interdisciplinary Perspectives on Infectious Diseases. 2008. 2008
- Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women.. The ISME (International Society for Microbial Ecology) Journal. 1:121-133. 2007
- MiCA: a web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes.. Microbial Ecology. 53. 2007
- Molecular genetics of Cicindela (Cylindera) terricola and elevation of C. lunalonga to species level, with comments on its conservation status. Conservation Genetics. 8:865-877. 2007
- Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics. 22. 2006
- From artificial evolution to computational evolution: a research agenda. Nature Reviews Genetics. 7:729-735. 2006
- Guidelines - From artificial evolution to computational evolution: a research agenda. Nature Reviews Genetics. 7:729-735. 2006
- Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method. Journal of Molecular Evolution. 62. 2006
- The vaginal flora of healthy women is not always dominated by Lactobacillus species. Journal of Infectious Diseases. 194:1468-1469. 2006
- Evolutionary computation for multiple sequence alignment. Genetic Programming and Evolvable Machines. 5:121-144. 2004
- Improving the Survivability of a Simple Evolved Circuit through Coevolution. 2004 NASA/DoD Conference on Evolvable Hardware. 123-129. 2004
- Multiple Sequence Alignment with Evolutionary Computation. Genetic Programming and Evolvable Machines. 5:121-144. 2004
- Special Issue on Biological Applications of Genetic and Evolutionary Computation. Genetic Programming and Evolvable Machines. 5. 2004
- Behavioral Diversity and a Probabilistically Optimal GP Ensemble. Genetic Programming and Evolvable Machines. 4:235-253. 2003
- Discipulus: the first commercial genetic programming system, invited publication. Genetic Programming and Evolvable Machines. 25:201-203. 2001
- Evolutionary computation.. Nature Reviews Genetics. 2:428-436. 2001
- Review: Discipulus: A Commercial Genetic Programming System. Genetic Programming and Evolvable Machines. 2:201-203. 2001
- The 2-pebbling property and a conjecture of Graham's. Graphs and Combinatorics. 16:231-244. 2000
- Special purpose image convolution with evolvable hardware. Lecture Notes in Computer Science. 1803:1-11. 2000
- Effects of Code Growth and Parsimony Pressure on Populations in Genetic Programming. Evolutionary Computation. 6:293-309. 1998
- Limiting code growth in genetic programming. Journal of Evolutionary Computation. 6:293-310. 1998
- Computer simulation of transposable element evolution: random template and strict master models. Journal of Molecular Evolution. 42:52-58. 1996
- (In-)Formal methods: Teaching program derivation via the Moore method. Computer Science Education. 6:67-91. 1995
- Exploring the polynomial hierarchy with generic sets. Journal of Computing and Information Technology. 166-183. 1995
- Using self-delimiting strings to represent trees. Congressus Numerantium. 107:5-22. 1995
- The Generic Oracle Hypothesis is False. Information Processing Letters. 45:59-62. 1993
- Representing arbitrary trees as self-delimiting binary strings. Congressus Numerantium. 96:47-56. 1993
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chapter
- An Evolutionary, Biosocial Perspective on Variation in Human Milk Microbes and Oligosaccharides: An Example of Eco-Homeorhesis?. Prebiotics and Probiotics in Human Milk: Origins and Functions of Milk-borne Oligosaccharides and Bacteria. Academic Press. 367-399. 2017
- tagged barcode analysis of microbial communities. Encyclopedia of Metagenomics. 2012
- Computational complexity and genetic algorithms. Advances in Fuzzy Systems and Evolutionary Computation. 248-253. 2001
- Genetic algorithms and hardness. Advances in Fuzzy Systems and Evolutionary Computation. 323-329. 2001
- The evolution of size and shape. Advances in Genetic Programming. 162-191. 1999
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conference paper
- Designer milk? Signatures of selection in human milk oligosaccharides. BEACON Congress. 2016
- Crossover Bias in Genetic Programming. Proceedings of the 10th European Conference on Genetic Programming. 33-44. 2007
- Co-evolving faults to improve the fault tolerance of sorting networks. Genetic Programming (EuroGP) 2004. Proceedings. 57-66. 2004
- Evolving better multiple sequence alignments. Genetic and Evolutionary Computation (GECCO) 2003. Proceedings. Part I. 449-460. 2004
- Inherent fault tolerance in evolved sorting networks. Genetic and Evolutionary Computation (GECCO) 2003. Proceedings. Part I. 456-457. 2003
- Evolving consensus sequence for multiple sequence alignment with a genetic algorithm. Genetic and Evolutionary Computation (GECCO) 2003. Proceedings. Part II. 2313-2324. 2003
- Electronic Polymerase Chain Reaction (EPCR) Search Algorithm. Proceedings of the IEEE 1st Bioinformatics Conference. 338-338. 2002
- MiCA: web-based computational tools for the analysis of microbial community structure and composition based on T-RFLP of 16S rRNA genes. Proceedings of the IEEE 1st Bioinformatics Conference. 341-341. 2002
- GABSyS: Using genetic algorithms to breed a combustion engine. International Conference on Evolutionary Computing. 259-264. 2002
- Representation and robustness for evolved sorting networks. 1st NASA/DoD Workshop on Evolvable Hardware. 255-261. 2002
- Size versus robustness in evolved sorting networks: is bigger better?. 2nd NASA/DoD Workshop on Evolvable Hardware. 81-90. 2002
- The test vector problem and limitations to evolving digital circuits. 2nd NASA/DoD Workshop on Evolvable Hardware. 75-80. 2002
- A genetic algorithm-specific test of random generator quality. 4th Annual Conference on Genetic and Evolutionary Computation. 691-691. 2002
- Abstention reduces errors: decision abstaining N-version genetic programming. 4th Annual Conference on Genetic and Evolutionary Computation. 796-803. 2002
- How random generator quality impacts genetic algorithm performance.. Proceedings of the International Conference on Genetic and Evolutionary Computation. 480-483. 2002
- N-Version Genetic Programming via Fault Masking. Genetic Programming (EuroGP) 2002. Proceedings. 172-181. 2002
- A genetic algorithm for expert system rule generation. Proceedings of the International Conference on Genetic and Evolutionary Computation. 757-757. 2001
- Computational complexity, genetic programming, and implications. Genetic Programming (EuroGP) 2001. Proceedings. 348-360. 2001
- Fault-tolerant computing with N-version genetic programming. Genetic and Evolutionary Computation Conference. 2001
- Fault-tolerant hardware through n-version genetic programming. 5th World Multiconference on Systematics, Cybernetics and Informatics. 2001
- Quantum evolutionary programming. Genetic and Evolutionary Computation Conference. 2001
- Evolving molecules for drug design using genetic algorithms via molecular trees. Genetic and Evolutionary Computation Conference. 2000
- GA hard problems. Genetic and Evolutionary Computation Conference. 2000
- Special purpose image convolution with evolvable hardware. Real-World Applications of Evolutionary Computing (EvoWorkshops) 2000. Proceedings. 1-11. 2000
- Providing support for multiple collection types in a fuzzy object oriented spatial data model. American Federation of Information Processing Societies. 1999
- Random number generator and GA performance revisisted. Genetic and Evolutionary Computation Conference. 425-432. 1999
- Random number generator and GP performance. Genetic and Evolutionary Computation Conference. 1999
- Toward byte code genetic programming. Genetic and Evolutionary Computation Conference. 1234-1234. 1999
- Using chaos in genetic algorithms. Genetic and Evolutionary Computation Conference. 2094-2101. 1999
- Finding cliques in Keller graphs with genetic algorithms. International Conference on Evolutionary Computing. 650-655. 1998
- Removal bias: A new cause of code growth in tree based evolutionary programming. 1998 IEEE International Conference on Evolutionary Computation - Proceedings. 781-786. 1998
- The efficient set GA for stock portfolios. International Conference on Evolutionary Computing. 354-359. 1998
- Code size and depth flows in genetic programming. International Conference on Genetic Programming. 313-320. 1997
- Genetic algorithm hardness measures applied to the maximum clique problem. International Conference on Genetic Algorithms. 81-88. 1997
- The effect of the quality of pseudo-random number generators on the performance of a simple genetic algorithm. International Conference on Genetic Algorithms. 276-282. 1997
- A Genetic algorithm solution to the efficient set problem: a technique for portfolio selection based on the Markowitz model. 1996 Annual Meeting, Decision Sciences Institute. 571-573. 1996
- Code growth in genetic programming. International Conference on Genetic Programming. 215-223. 1996
- Using genetic programming to approximate maximum cliques. International Conference on Genetic Programming. 400-405. 1996
- A highly compact representation of tree structures (abstract). Data Compression Conference. 453-453. 1993
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editorial article
- Introduction to special section: Best of EuroGP/EvoBio. Genetic Programming and Evolvable Machines. 14:429-430. 2013
- Guest editorial: special issue on selected papers from the European conference on genetic programming. Genetic Programming and Evolvable Machines. 13:271-273. 2012
- Introduction. Genetic Programming and Evolvable Machines. 6:5-6. 2005