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1. Full Text Adherence issues related to sublingual immunotherapy as perceived by allergists
by Scurati, Silvia and Frati, Franco and Passalacqua, Gianni and Puccinelli, Paola and Hilaire, Cecile and Incorvaia, Cristoforo and D'Avino, Gennaro and Comi, Rosa and Lo Schiavo, Mario and Pezzuto, Francesco and Montera, Carmen and Pio, Antonio and Teresa Ielpo, Maria and Cellini, Francesco and Vicentini, Licia and Pecorari, Roberto and Aresu, Tiziana and Capra, Lucetta and De Benedictis, Elena and Bombi, Claudio and Zauli, Daniela and Vanzi, Annarita and Alberto Paltrinieri, Carlo and Bondioli, Alfeo and Paletta, Isabella and Ventura, Domenica and Mei, Francesco and Paolini, Franco and Colangelo, Caterina and Cavallucci, Enrico and Cucinelli, Francesco and Tinari, Rosanna and Ermini, Giuseppe and Beltrami, Valerio and Novembre, Elio and Begliomini, Cinzia and Marchese, Erminia and Solito, Enrico and Ammannati, Valentino and Molino, Gaetanino and Galli, Elena and Baldassini, Mauro and Di Michele, Loreta and Calvani, Mauro and Gidaro, Mirella and Venuti, Alberto and Li Bianchi, Enrico and Benassi, Fulvio and Pocobelli, Donatella and Zangari, Paola and De Rocco, Maria Grazia and Lo Vecchio, Antonella and Pingitore, Giuseppe and Grimaldi, Orazio and Schiavino, Domenico and Perrone, Nicola and Antonietta Frieri, Maria and Di Rienzo, Valerio and Tripodi, Salvatore and Scarpa, Alessandro and Tomsic, Mirala and Bonaguro, Roberta and Enrico Senna, Gian and Sirena, Alberto and Turatello, Franca and Crescioli, Stefano and Favero, Elisabetta and Billeri, Lucia and Chieco Bianchi, Fulvia and Gemignani, Carla and Zanforlin, Mario and Angiola Crivellaro, Maria and Hendrick, Birgir and Maltauro, Adriana and Masieri, Simonetta and Elisabetta Conte, Maria and Fama, Mario and Pozzan, Marcella and Bonadonna, Patrizia and Casanova, Stefania and Vallerani, Elisabetta and Schiappoli, Michele and Borghesan, Franco and Giro, Giuseppina and Casotto, Stefano and Berardino, Loredana and Zanoni, Giovanna and Ariano, Renato and Aquilina, Riccardo and Pellegrino, Renato and Marsico, Pietro and Del Giudice, Angelica and Narzisi, Giuseppe and Tomaselli, Valerio and Fornaca, Gianfranco and Favro, Mauro and Loperfido, Bruna and Gallo, Cesare and Buffoni, Sebastiano and Gani, Federica and ... and Italian Study Grp SLIT Compliance
Patient Preference and Adherence, ISSN 1177-889X, 2010, Volume 4, pp. 141 - 145
Objectives: Sublingual immunotherapy (SLIT) is a viable alternative to subcutaneous immunotherapy to treat allergic rhinitis and asthma, and is widely used in... 
Adherence | Efficacy | Side effects | Cost | Sublingual immunotherapy | cost | adherence | SLIT FORMULATION | HOUSE-DUST MITE | efficacy | CHILDREN | RHINITIS | MEDICINE, GENERAL & INTERNAL | IMPACT | EASY PROJECT | QUANTITATIVE ASSESSMENT | side effects | ASTHMA | sublingual immunotherapy | GALEN | LIFE | Perceptions | Immunotherapy
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2. Full Text Clonal selection: an immunological algorithm for global optimization over continuous spaces
by Pavone, Mario and Narzisi, Giuseppe and Nicosia, Giuseppe
Journal of Global Optimization, ISSN 0925-5001, 8/2012, Volume 53, Issue 4, pp. 769 - 808
In this research paper we present an immunological algorithm (IA) to solve global numerical optimization problems for high-dimensional instances. Such... 
Global optimization | Immunological algorithms | Operations Research/Decision Theory | Nonlinear optimization | Black-box optimization | Evolutionary algorithms | Computer Science, general | Optimization | Economics / Management Science | Real Functions | Derivative-free optimization | MATHEMATICS, APPLIED | OPERATIONS RESEARCH & MANAGEMENT SCIENCE | TIME | ARTIFICIAL IMMUNE-SYSTEMS | Computer science | Mathematical optimization | Algorithms | Studies
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3. Full Text A multi-objective evolutionary approach to the protein structure prediction problem
by Vincenzo Cutello and Giuseppe Narzisi and Giuseppe Nicosia
Journal of The Royal Society Interface, ISSN 1742-5689, 02/2006, Volume 3, Issue 6, pp. 139 - 151
(bond atoms) and 
Pareto front | Multi-objective optimization | Protein structure prediction | Multi-objective evolutionary algorithms | Protein folding | multi-objective evolutionary algorithms | MULTIDISCIPLINARY SCIENCES | RESOLUTION | SIMULATION | GENETIC ALGORITHM | NUCLEIC-ACIDS | SEQUENCE | FORCE-FIELD | protein folding | SECONDARY STRUCTURE | multi-objective optimization | protein structure prediction | Amino Acid Sequence | Sequence Alignment - methods | Sequence Analysis, Protein - methods | Algorithms | Models, Chemical | Computer Simulation | Models, Molecular | Molecular Sequence Data | Protein Conformation | Proteins - chemistry | Proteins - ultrastructure | Evolution, Molecular
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4. Full Text Comparing De Novo genome assembly: The long and short of it
by Narzisi, Giuseppe and Mishra, Bud
PLoS ONE, ISSN 1932-6203, 2011, Volume 6, Issue 4, p. e19175
Recent advances in DNA sequencing technology and their focal role in Genome Wide Association Studies (GWAS) have rekindled a growing interest in the... 
MILLIONS | MULTIDISCIPLINARY SCIENCES | SHORT DNA-SEQUENCES | APPROXIMATION ALGORITHM | VIRULENCE | READS | PROGRAM | GRAPHS | Computational Biology - methods | Genome, Bacterial | Reproducibility of Results | Genomics | Humans | Genetic Techniques | Biotechnology - methods | Algorithms | ROC Curve | Software | Genome | Genome, Human | Genome-Wide Association Study - methods | Sequence Analysis, DNA - methods | Genomes | Nucleotide sequencing | Analysis | DNA sequencing | Haplotypes | Nucleotide sequence | Encyclopedias | Software development tools | Source code | Gene sequencing | Consortia | Freeware | Accuracy | Microorganisms | E coli | Technology | Wolbachia | Computer applications | Problem solving | Life sciences | Trends | Bioinformatics | Assembly | Deoxyribonucleic acid--DNA | Deoxyribonucleic acid | DNA
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5. Full Text The contribution of de novo coding mutations to autism spectrum disorder
by Iossifov, Ivan and Iossifov, Ivan and O'Roak, Brian J and Sanders, Stephan J and Ronemus, Michael and Krumm, Niklas and Levy, Dan and Stessman, Holly A and Witherspoon, Kali T and Vives, Laura and Patterson, Karynne E and Smith, Joshua D and Paeper, Bryan and Nickerson, Deborah A and Dea, Jeanselle and Dong, Shan and Gonzalez, Luis E and Mandell, Jeffrey D and Mane, Shrikant M and Murtha, Michael T and Sullivan, Catherine A and Walker, Michael F and Waqar, Zainulabedin and Wei, Liping and Willsey, A. Jeremy and Yamrom, Boris and Lee, Yoon-Ha and Grabowska, Ewa and Dalkic, Ertugrul and Wang, Zihua and Marks, Steven and Andrews, Peter and Leotta, Anthony and Kendall, Jude and Hakker, Inessa and Rosenbaum, Julie and Ma, Beicong and Rodgers, Linda and Troge, Jennifer and Narzisi, Giuseppe and Yoon, Seungtai and Schatz, Michael C and Ye, Kenny and McCombie, W. Richard and Shendure, Jay and Eichler, Evan E and State, Matthew W and Wigler, Michael
Nature, ISSN 0028-0836, 11/2014, Volume 515, Issue 7526, pp. 216 - 221
Whole exome sequencing has proven to be a powerful tool for understanding the genetic architecture of human disease. Here we apply it to more than 2,500... 
INTELLECTUAL DISABILITY | INHERITED DISEASE | NETWORK | EVOLUTION | MULTIDISCIPLINARY SCIENCES | PATERNAL AGE | SCHIZOPHRENIA | RISK | STRUCTURAL VARIATION | COPY-NUMBER VARIATION | RESOURCE | Genetic Predisposition to Disease - genetics | Reproducibility of Results | Genes | Humans | Male | Mutation - genetics | Open Reading Frames - genetics | Intelligence Tests | Exome - genetics | Child Development Disorders, Pervasive - genetics | Female | Child | Cluster Analysis | Gene mutations | Analysis | Pervasive developmental disorders | Research | Nucleotide sequencing | Health aspects | DNA sequencing | Autism | Mutation | Siblings
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6. Full Text Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons
by Vezzi, Francesco and Narzisi, Giuseppe and Mishra, Bud and Science for Life Laboratory, SciLifeLab and KTH and Centra
PLoS ONE, ISSN 1932-6203, 12/2012, Volume 7, Issue 12, p. e52210
In just the last decade, a multitude of bio-technologies and software pipelines have emerged to revolutionize genomics. To further their central goal, they aim... 
READ ALIGNMENT | MULTIDISCIPLINARY SCIENCES | Computational Biology - methods | Software | Algorithms | Sequence Analysis, DNA - methods | Genomes | Nucleotide sequencing | Analysis | Genomics | DNA sequencing | Nucleotide sequence | Laboratories | Pipelines | Biology | Research | Gene sequencing | Datasets | Studies | Problems | Motivation | Graphs | Assemblies | Bioinformatics | Assembly | Deoxyribonucleic acid--DNA | Biological Sciences | sequence alignment | sensitivity analysis | data processing | DNA sequence | genetic database | article | genetic algorithm | Naturvetenskap | Biologiska vetenskaper | bioinformatics | reference value | genomics | contig mapping | Natural Sciences | feature response curve | intermethod comparison | Deoxyribonucleic acid | DNA
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7. Full Text De Novo Gene Disruptions in Children on the Autistic Spectrum
by Iossifov, Ivan and Ronemus, Michael and Levy, Dan and Wang, Zihua and Hakker, Inessa and Rosenbaum, Julie and Yamrom, Boris and Lee, Yoon-ha and Narzisi, Giuseppe and Leotta, Anthony and Kendall, Jude and Grabowska, Ewa and Ma, Beicong and Marks, Steven and Rodgers, Linda and Stepansky, Asya and Troge, Jennifer and Andrews, Peter and Bekritsky, Mitchell and Pradhan, Kith and Ghiban, Elena and Kramer, Melissa and Parla, Jennifer and Demeter, Ryan and Fulton, Robert S and Fulton, Lucinda L and Magrini, Vincent J and Ye, Kenny and Darnell, Jennifer C and Darnell, Robert B and Mardis, Elaine R and Wilson, Richard K and Schatz, Michael C and McCombie, W. Richard and Wigler, Michael
Neuron, ISSN 0896-6273, 04/2012, Volume 74, Issue 2, pp. 285 - 299
Exome sequencing of 343 families, each with a single child on the autism spectrum and at least one unaffected sibling, reveal de novo small indels and point... 
NETWORK | DYRK1A | RIM1-ALPHA | IDENTIFICATION | NEUROSCIENCES | COPY-NUMBER VARIATION | REGION | PARADIGM | RESOURCE | Genetic Predisposition to Disease | Genetic Association Studies | Humans | Parents | Child, Preschool | Models, Molecular | Child Development Disorders, Pervasive - etiology | Family Health | Male | Gene Dosage | Mutation - genetics | Phenotype | Child Development Disorders, Pervasive - genetics | Female | Fragile X Mental Retardation Protein - genetics | Child | Autism | Genes | Disease susceptibility | Mutation | Siblings
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8. Full Text Feature-by-feature - evaluating De Novo sequence assembly
by Vezzi, Francesco and Narzisi, Giuseppe and Mishra, Bud
PLoS ONE, ISSN 1932-6203, 02/2012, Volume 7, Issue 2, p. e31002
The whole-genome sequence assembly (WGSA) problem is among one of the most studied problems in computational biology. Despite the availability of a plethora of... 
MULTIDISCIPLINARY SCIENCES | Computational Biology - methods | Contig Mapping | Genome | Sequence Analysis, DNA - methods | Methods | Analysis | Genomics | Genomes | Nucleotide sequence | Computer simulation | Independent component analysis | Principal components analysis | Biology | Medicine | Engineering | Brain research | Algorithms | Simulation | Correlation analysis | Flight simulators | Computer applications | Gauging | Software | International conferences | Gaging | Quality assessment | Simulators | Bioinformatics | Assembly
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9. Full Text Accurate de novo and transmitted indel detection in exome-capture data using microassembly
by Narzisi, Giuseppe and Narzisi, Giuseppe and O'Rawe, Jason A and Iossifov, Ivan and Fang, Han and Lee, Yoon-Ha and Wang, Zihua and Wu, Yiyang and Lyon, Gholson J and Wigler, Michael and Schatz, Michael C
Nature Methods, ISSN 1548-7091, 01/2014, Volume 11, Issue 10, pp. 1033 - 1036
We present an open-source algorithm, Scalpel (http://scalpel.sourceforge.net/), which combines mapping and assembly for sensitive and specific discovery of... 
AUTISM | HUMAN GENOMES | VARIANTS | SNP | BIOCHEMICAL RESEARCH METHODS | MUTATIONS | SPECTRUM | DELETIONS | INSERTIONS | READS | Exome | Computational Biology - methods | DNA - chemistry | Sequence Alignment | Algorithms | Humans | Databases, Genetic | Programming Languages | Software | Mutation | DNA Mutational Analysis - methods | INDEL Mutation | Usage | Physiological aspects | Research | Single nucleotide polymorphisms | Genetic screening | Methods | Genetic algorithms | Genomics | Deoxyribonucleic acid--DNA
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10. Full Text Clonal selection algorithms: A comparative case study using effective mutation potentials
by Cutello, Vincenzo and Narzisi, Giuseppe and Nicosia, Giuseppe and Pavone, Mario
Lecture Notes in Computer Science, ISSN 0302-9743, 2005, Volume 3627, pp. 13 - 28
This paper presents a comparative study of two important Clonal Selection Algorithms (CSAs): CLONALG and opt-IA. To deeply understand the performance of both... 
One-counting | Trap functions | Numerical optimization | NP-complete problems | CLONALG | Pattern recognition | Opt-IA | 2D HP Protein Structure Prediction | Clonal Selection Algorithms | onecounting | COMPUTER SCIENCE, THEORY & METHODS | opt-IA | trap functions | 2D HP protein structure prediction | numerical optimization | OPERATORS | pattern recognition
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11. Full Text The challenge of small-scale repeats for indel discovery
by Narzisi, Giuseppe and Schatz, Michael C
Frontiers in Bioengineering and Biotechnology, ISSN 2296-4185, 2015, Volume 3, p. 8
Repetitive sequences are abundant in the human genome. Different classes of repetitive DNA sequences, including simple repeats, tandem repeats, segmental... 
Sequence assembly | Next-generation sequencing | Repetitive sequences | Sequence analysis | Nucleic acid | Variant detection | Indel mutation | Repetitive Sequences, Nucleic Acid | Sequence Analysis | INDEL Mutation
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12. Full Text Indel variant analysis of short-read sequencing data with Scalpel
by Fang, Han and Bergmann, Ewa A and Arora, Kanika and Vacic, Vladimir and Zody, Michael C and Iossifov, Ivan and O'rawe, Jason A and Wu, Yiyang and Jimenez Barron, Laura T and Rosenbaum, Julie and Ronemus, Michael and Lee, Yoon-Ha and Wang, Zihua and Dikoglu, Esra and Jobanputra, Vaidehi and Lyon, Gholson J and Wigler, Michael and Schatz, Michael C and Narzisi, Giuseppe
Nature Protocols, ISSN 1754-2189, 12/2016, Volume 11, Issue 12, pp. 2529 - 2548
As the second most common type of variation in the human genome, insertions and deletions (indels) have been linked to many diseases, but the discovery of... 
DE-NOVO | MUTATION-RATE | BIOCHEMICAL RESEARCH METHODS | FRAMEWORK | VARIATION DISCOVERY | DELETIONS | INSERTIONS | GENOME | Genomics | Humans | Molecular Sequence Annotation | Alleles | Polymorphism, Single Nucleotide | DNA Mutational Analysis - methods | High-Throughput Nucleotide Sequencing - methods | INDEL Mutation | Nucleotide sequencing | Gene mutations | Genetic variation | Identification and classification | Methods | DNA sequencing
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13. Full Text Scoring-and-unfolding trimmed tree assembler: Concepts, constructs and comparisons
by Narzisi, Giuseppe and Mishra, Bud
Bioinformatics, ISSN 1367-4803, 01/2011, Volume 27, Issue 2, pp. 153 - 160
Motivation: Mired by its connection to a well-known NP-complete combinatorial optimization problem-namely, the Shortest Common Superstring Problem... 
ALGORITHMS | MILLIONS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENOME | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Genome, Bacterial | Software | Algorithms | Genomics - methods | Sequence Analysis, DNA - methods
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14. Full Text A class of Pareto Archived Evolution Strategy algorithms using immune inspired operators for Ab-Initio Protein Structure Prediction
by Cutello, Vincenzo and Narzisi, Giuseppe and Nicosia, Giuseppe
Lecture Notes in Computer Science, ISSN 0302-9743, 2005, Volume 3449, pp. 54 - 63
In this work we investigate the applicability of a multiobjective formulation of the Ab-Initio Protein Structure Prediction (PSP) to medium size protein... 
Clonal selection principle | Tertiary fold prediction | Multi-objective evolutionary algorithms | Hypermutation operators | Protein structure | Genetic algorithms | protein structure | multi-objective evolutionary algorithms | hypermutation operators | COMPUTER SCIENCE, THEORY & METHODS | genetic algorithms | tertiary fold prediction | clonal selection principle | GENETIC ALGORITHM
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15. Full Text Reducing INDEL calling errors in whole genome and exome sequencing data
by Fang, Han and Wu, Yiyang and Narzisi, Giuseppe and O'Rawe, Jason A and Barrón, Laura T.Jimenez and Rosenbaum, Julie and Ronemus, Michael and Iossifov, Ivan and Schatz, Michael C and Lyon, Gholson J
Genome Medicine, ISSN 1756-994X, 10/2014, Volume 6, Issue 10, pp. 89 - 89
Background: INDELs, especially those disrupting protein-coding regions of the genome, have been strongly associated with human diseases. However, there are... 
SMALL INSERTIONS | READ | DE-NOVO