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1. Full Text BUSCA: an integrative web server to predict subcellular localization of proteins
by Savojardo, Castrense and Martelli, Pier Luigi and Fariselli, Piero and Profiti, Giuseppe and Casadio, Rita
Nucleic Acids Research, ISSN 0305-1048, 07/2018, Volume 46, Issue W1, pp. W459 - W466
Abstract Here, we present BUSCA (http://busca.biocomp.unibo.it), a novel web server that integrates different computational tools for predicting protein... 
BIOCHEMISTRY & MOLECULAR BIOLOGY | SEQUENCE | Web Server Issue
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2. Full Text Cost-Effectiveness of Axicabtagene Ciloleucel for Relapsed or Refractory Dffuse Large B-Cell Lymphoma in Italy
by Marchetti, Monia and Martelli, Elisa and Zinzani, Pier Luigi
Blood, ISSN 0006-4971, 11/2018, Volume 132, Issue Supplement 1, pp. 4779 - 4779
Abstract BACKGROUND: Axicabtagene ciloleucel (axi-cel) is a CD19-directed chimeric antigenic receptor (CAR) T-cell therapy which has been approved by FDA for... 
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3. Full Text PhenPath: a tool for characterizing biological functions underlying different phenotypes
by Babbi, G and Martelli, PL and Casadio, R
BMC GENOMICS, ISSN 1471-2164, 07/2019, Volume 20, Issue Suppl 8, pp. 548 - 11
BackgroundMany diseases are associated with complex patterns of symptoms and phenotypic manifestations. Parsimonious explanations aim at reconciling the... 
Enrichment | OVARY | POPULATION | RETT-SYNDROME | Diseases | Phenotype | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DISEASE | GENES | GENETICS & HEREDITY | MUTATIONS | Molecular pathway | Biological process | ASSOCIATION | Symptomatology | Usage | Physicians | Analysis | Practice | Research | Molecular biology
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4. Full Text SChloro: directingViridiplantaeproteins to six chloroplastic sub-compartments
by Savojardo, Castrense and Martelli, Pier Luigi and Fariselli, Piero and Casadio, Rita
Bioinformatics, ISSN 1367-4803, 10/2016, p. btw656
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5. Full Text Assessment of methods for predicting the effects of PTEN and TPMT protein variants
by Pejaver, Vikas and Babbi, Giulia and Casadio, Rita and Folkman, Lukas and Katsonis, Panagiotis and Kundu, Kunal and Lichtarge, Olivier and Martelli, Pier Luigi and Miller, Maximilian and Moult, John and Pal, Lipika R and Savojardo, Castrense and Yin, Yizhou and Zhou, Yaoqi and Radivojac, Predrag and Bromberg, Yana
Human Mutation, ISSN 1059-7794, 09/2019, Volume 40, Issue 9, pp. 1495 - 1506
Thermodynamic stability is a fundamental property shared by all proteins. Changes in stability due to mutation are a widespread molecular mechanism in genetic... 
variant stability profiling | phosphatase and tensin homolog, PTEN | VAMP‐seq | thiopurine S‐methyl transferase, TPMT | CAGI | MUTAGENESIS | TPMT | PTEN | STABILITY CHANGES | MISSENSE VARIANT | phosphatase and tensin homolog | thiopurine S-methyl transferase | PATHOGENICITY | THERMODYNAMICS | SEQUENCE | MUTATION | GENETICS & HEREDITY | VAMP-seq | BINDING | WEB SERVER | Proteins | Phosphatases | Analysis | Genomics | Methods | Genomes | Mutation | PTEN protein | Computer applications
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6. Full Text Assessing predictions on fitness effects of missense variants in calmodulin
by Zhang, Jing and Kinch, Lisa N and Cong, Qian and Katsonis, Panagiotis and Lichtarge, Olivier and Savojardo, Castrense and Babbi, Giulia and Martelli, Pier Luigi and Capriotti, Emidio and Casadio, Rita and Garg, Aditi and Pal, Debnath and Weile, Jochen and Sun, Song and Verby, Marta and Roth, Frederick P and Grishin, Nick V
Human Mutation, ISSN 1059-7794, 09/2019, Volume 40, Issue 9, pp. 1463 - 1473
This paper reports the evaluation of predictions for the “CALM1” challenge in the fifth round of the Critical Assessment of Genome Interpretation held in 2018.... 
predictors | disease | calmodulin | missense variants | CAGI | EVOLUTIONARY | ACTIVATION | RECOGNITION | CATALOG | DATABASE | SEQUENCE | GENETICS & HEREDITY | MUTATIONS | BINDING | Analysis | Calmodulin | Conserved sequence | Genomes | Calcium-binding protein | Fitness
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7. Full Text Assessing predictions of the impact of variants on splicing in CAGI5
by Mount, Stephen M and Avsec, Žiga and Carmel, Liran and Casadio, Rita and Çelik, Muhammed Hasan and Chen, Ken and Cheng, Jun and Cohen, Noa E and Fairbrother, William G and Fenesh, Tzila and Gagneur, Julien and Gotea, Valer and Holzer, Tamar and Lin, Chiao‐Feng and Martelli, Pier Luigi and Naito, Tatsuhiko and Nguyen, Thi Yen Duong and Savojardo, Castrense and Unger, Ron and Wang, Robert and Yang, Yuedong and Zhao, Huiying
Human Mutation, ISSN 1059-7794, 09/2019, Volume 40, Issue 9, pp. 1215 - 1224
Precision medicine and sequence‐based clinical diagnostics seek to predict disease risk or to identify causative variants from sequencing data. The Critical... 
CAGI experiment | mutation | splicing | machine learning | variant interpretation | GENETIC-VARIATION | RNA | GENETICS & HEREDITY | MECHANISMS | MISSENSE MUTATIONS | Analysis | Genomics | Machine learning | Phenotypes | Genomes | Splicing | Genotypes
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8. Full Text Assessing computational predictions of the phenotypic effect of cystathionine‐beta‐synthase variants
by Kasak, Laura and Bakolitsa, Constantina and Hu, Zhiqiang and Yu, Changhua and Rine, Jasper and Dimster‐Denk, Dago F and Pandey, Gaurav and Baets, Greet and Bromberg, Yana and Cao, Chen and Capriotti, Emidio and Casadio, Rita and Durme, Joost and Giollo, Manuel and Karchin, Rachel and Katsonis, Panagiotis and Leonardi, Emanuela and Lichtarge, Olivier and Martelli, Pier Luigi and Masica, David and Mooney, Sean D and Olatubosun, Ayodeji and Radivojac, Predrag and Rousseau, Frederic and Pal, Lipika R and Savojardo, Castrense and Schymkowitz, Joost and Thusberg, Janita and Tosatto, Silvio C.E and Vihinen, Mauno and Väliaho, Jouni and Repo, Susanna and Moult, John and Brenner, Steven E and Friedberg, Iddo
Human Mutation, ISSN 1059-7794, 09/2019, Volume 40, Issue 9, pp. 1530 - 1545
Accurate prediction of the impact of genomic variation on phenotype is a major goal of computational biology and an important contributor to personalized... 
critical assessment | phenotype prediction | machine learning | cystathionine‐beta‐synthase | CAGI challenge | single amino acid substitution | cystathionine-beta-synthase | CLASSIFICATION | SNAP | IMPACT | PATHOGENICITY | ENZYME | SERVER | GENETICS & HEREDITY | MUTATIONS | PROTEIN FUNCTION | TOOLS | Enzymes | Medical colleges | Homocysteine | Analysis | Genomics | Machine learning | Amino acids | Homocystinuria | Phenotypes | Computer applications | Phenotypic variations
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9. Full Text SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments
by Savojardo, Castrense and Martelli, Pier Luigi and Fariselli, Piero and Casadio, Rita
Bioinformatics (Oxford, England), ISSN 1367-4803, 02/2017, Volume 33, Issue 3, pp. 347 - 353
Chloroplasts are organelles found in plants and involved in several important cell processes. Similarly to other compartments in the cell, chloroplasts have an... 
Sequence Analysis, Protein - methods | Computational Biology - methods | Viridiplantae - metabolism | Membrane Proteins - metabolism | Plant Proteins - metabolism | Software | Machine Learning | Chloroplasts - metabolism | Protein Transport | Original Papers
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10. Full Text Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer
by Voskanian, Alin and Katsonis, Panagiotis and Lichtarge, Olivier and Pejaver, Vikas and Radivojac, Predrag and Mooney, Sean D and Capriotti, Emidio and Bromberg, Yana and Wang, Yanran and Miller, Max and Martelli, Pier Luigi and Savojardo, Castrense and Babbi, Giulia and Casadio, Rita and Cao, Yue and Sun, Yuanfei and Shen, Yang and Garg, Aditi and Pal, Debnath and Yu, Yao and Huff, Chad D and Tavtigian, Sean V and Young, Erin and Neuhausen, Susan L and Ziv, Elad and Pal, Lipika R and Andreoletti, Gaia and Brenner, Steven E and Kann, Maricel G
Human Mutation, ISSN 1059-7794, 09/2019, Volume 40, Issue 9, pp. 1612 - 1622
The availability of disease‐specific genomic data is critical for developing new computational methods that predict the pathogenicity of human variants and... 
breast cancer | SNV | CHEK2 | Hispanic women | CAGI | EVOLUTIONARY ACTION | PROTEIN | MISSENSE SUBSTITUTIONS | RISK | CLASSIFICATION | DISEASE-RELATED MUTATIONS | MATRICES | GENETICS & HEREDITY | GENERATION | UNIREF | SEQUENCE-ALIGNMENT | Hispanic American women | Analysis | Genomics | Genetic research | Breast cancer | Genetic aspects | Methods | Cancer | Pathogenicity | CHK2 protein | Computer applications | Genomes | Kinases | Generalized linear models
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11. Full Text CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases
by Kasak, Laura and Hunter, Jesse M and Udani, Rupa and Bakolitsa, Constantina and Hu, Zhiqiang and Adhikari, Aashish N and Babbi, Giulia and Casadio, Rita and Gough, Julian and Guerrero, Rafael F and Jiang, Yuxiang and Joseph, Thomas and Katsonis, Panagiotis and Kotte, Sujatha and Kundu, Kunal and Lichtarge, Olivier and Martelli, Pier Luigi and Mooney, Sean D and Moult, John and Pal, Lipika R and Poitras, Jennifer and Radivojac, Predrag and Rao, Aditya and Sivadasan, Naveen and Sunderam, Uma and Saipradeep, V. G and Yin, Yizhou and Zaucha, Jan and Brenner, Steven E and Meyn, M. Stephen
Human Mutation, ISSN 1059-7794, 09/2019, Volume 40, Issue 9, pp. 1373 - 1391
Whole‐genome sequencing (WGS) holds great potential as a diagnostic test. However, the majority of patients currently undergoing WGS lack a molecular... 
phenotype prediction | whole‐genome sequencing data | SickKids | pediatric rare disease | variant interpretation | CAGI | INDUCE | DISTINCT | EP300 MUTATION | GENE | DYSTROPHY | whole-genome sequencing data | EXPANSION | GENETICS & HEREDITY | Medical research | Anopheles | Genes | Genomics | Medicine, Experimental | Genetic aspects | Children | Nucleotide sequencing | Diseases | DNA sequencing | Pathogenicity | Genotype & phenotype | Phenotypes | Genomes
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12. Full Text A sequence-profile-based HMM for predicting and discriminating β barrel membrane proteins
by Martelli, Pier Luigi and Fariselli, Piero and Krogh, Anders and Casadio, Rita
Bioinformatics, ISSN 1367-4803, 2002, Volume 18, Issue 1, pp. S46 - S52
Membrane proteins are an abundant and functionally relevant subset of proteins that putatively include from about 15 up to 30% of the proteome of organisms... 
HMM | Outer membrane protein topology | Protein structure prediction | β barrel membrane proteins | Genome analysis | Sequence Homology, Amino Acid | Sequence Alignment - methods | Sequence Analysis, Protein - methods | Markov Chains | Algorithms | Membrane Proteins - chemistry | Models, Chemical | Models, Molecular | Membrane Proteins - classification | Models, Statistical
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13. Full Text A natural upper bound to the accuracy of predicting protein stability changes upon mutations
by Montanucci, Ludovica and Martelli, Pier Luigi and Ben-Tal, Nir and Fariselli, Piero
Bioinformatics (Oxford, England), ISSN 1367-4803, 05/2019, Volume 35, Issue 9, pp. 1513 - 1517
Accurate prediction of protein stability changes upon single-site variations (ΔΔG) is important for protein design, as well as for our understanding of the... 
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14. Full Text How to inherit statistically validated annotation within BAR+ protein clusters
by Piovesan, Damiano and Martelli, Pier Luigi and Fariselli, Piero and Profiti, Giuseppe and Zauli, Andrea and Rossi, Ivan and Casadio, Rita
BMC Bioinformatics, ISSN 1471-2105, 02/2013, Volume 14, Issue 3, pp. S4 - S4
In the genomic era a key issue is protein annotation, namely how to endow protein sequences, upon translation from the corresponding genes, with structural and... 
Proteins - genetics | Proteins - physiology | Sequence Analysis, Protein | Data Interpretation, Statistical | Vocabulary, Controlled | Databases, Protein | Genomics | Molecular Sequence Annotation | Cluster Analysis | Proteins | Studies | Automation | Ontology | Bioinformatics | Methods
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15. Full Text PredGPI: A GPI-anchor predictor
by Pierleoni, Andrea and Martelli, Pier and Casadio, Rita
BMC Bioinformatics, ISSN 1471-2105, 09/2008, Volume 9, Issue 1, pp. 392 - 392
Background: Several eukaryotic proteins associated to the extracellular leaflet of the plasma membrane carry a Glycosylphosphatidylinositol (GPI) anchor, which... 
TOPOLOGY | SEQUENCES | BIOCHEMICAL RESEARCH METHODS | IDENTIFICATION | SACCHAROMYCES-CEREVISIAE | MAMMALIAN-CELLS | PLASMA-MEMBRANE | MODIFICATION SITES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | GENOME-WIDE | ARABIDOPSIS | MEMBRANE-PROTEINS | Amino Acid Sequence | Sequence Analysis, Protein - methods | Algorithms | Glycosylphosphatidylinositols - chemistry | Models, Chemical | Computer Simulation | Molecular Sequence Data | Software | Protein research | Cellular proteins | Properties | Methods
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16. Full Text Functional annotations improve the predictive score of human disease‐related mutations in proteins
by Calabrese, Remo and Capriotti, Emidio and Fariselli, Piero and Martelli, Pier Luigi and Casadio, Rita
Human Mutation, ISSN 1059-7794, 08/2009, Volume 30, Issue 8, pp. 1237 - 1244
Single nucleotide polymorphisms (SNPs) are the simplest and most frequent form of human DNA variation, also valuable as genetic markers of disease... 
support vector machine | missense mutation | Gene Ontology | disease‐related SNP | Gene ontology | Missense mutation | Support vector machine | Disease-related SNP | disease-related SNP | SUPPORT VECTOR MACHINES | HUMAN SNPS | TERMS | MISSENSE MUTATIONS | EVOLUTIONARY INFORMATION | HUMAN GENOME | DATABASE | GENETICS & HEREDITY | SEQUENCE-ALIGNMENT | SINGLE-NUCLEOTIDE POLYMORPHISMS | Proteins - genetics | Mutation | Humans | Abnormalities, Multiple - genetics | Syndrome
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17. Full Text INPS-MD: a web server to predict stability of protein variants from sequence and structure: Table 1
by Savojardo, Castrense and Fariselli, Piero and Martelli, Pier Luigi and Casadio, Rita
Bioinformatics, ISSN 1367-4803, 08/2016, Volume 32, Issue 16, pp. 2542 - 2544
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18. Full Text DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks
by Savojardo, Castrense and Bruciaferri, Niccolò and Tartari, Giacomo and Martelli, Pier Luigi and Casadio, Rita
Bioinformatics, ISSN 1367-4803, 06/2019
Abstract Motivation The correct localization of proteins in cell compartments is a key issue for their function. Particularly, mitochondrial proteins are... 
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19. Full Text INPS-MD: A web server to predict stability of protein variants from sequence and structure
by Savojardo, Castrense and Fariselli, Piero and Martelli, Pier Luigi and Casadio, Rita
Bioinformatics, ISSN 1367-4803, 08/2016, Volume 32, Issue 16, pp. 2542 - 2544
Motivation: Protein function depends on its structural stability. The effects of single point variations on protein stability can elucidate the molecular... 
BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Computers | Proteins | Amino Acid Sequence | Sequence Analysis, Protein | Humans | Software | Protein Stability
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20. Full Text INPS: Predicting the impact of non-synonymous variations on protein stability from sequence
by Fariselli, Piero and Martelli, Pier Luigi and Savojardo, Castrense and Casadio, Rita
Bioinformatics, ISSN 1367-4803, 02/2015, Volume 31, Issue 17, pp. 2816 - 2821
Motivation: A tool for reliably predicting the impact of variations on protein stability is extremely important for both protein engineering and for... 
MUTANTS | BIOINFORMATICS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SERVER | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | NETWORKS | MUTATIONS | POTENTIALS | AMINO-ACID SUBSTITUTION | Computational Biology - methods | Humans | Mutation - genetics | Machine Learning | Tumor Suppressor Protein p53 - genetics | Proteins - genetics | Thermodynamics | Algorithms | Protein Engineering | Software | Tumor Suppressor Protein p53 - chemistry | Protein Stability | Proteins - chemistry | High-Throughput Nucleotide Sequencing - methods | Proteins | Mutations | State of the art | Stability | Regression | Tools | Sequencing | Bioinformatics
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