Publications
Publications
on Journals
- Fariselli
P, Compiani M, Casadio R - Predicting secondary structures of membrane
proteins with neural networks- Eur Biophys J 22: 41-51 (1993)
- Fariselli
P, Di Bernardo S, Casadio R - A mathematical model relating diffusion of
hydrophobic ions to their adsorption on biological membranes as detected
with a microdialyzer- J Biol Phys 19: 211-222 (1994)
- Rost B,
Casadio R, Fariselli P, Sander C - Transmembrane helices predicted at 95%
accuracy- Protein Science 4, 521-533 (1995)
- Vivarelli
F, Giusti G, Villani M, Campanini R, Fariselli P, Compiani M, Casadio R
-LGANN: a parallel system combining a local genetic algorithm and neural
networks for the prediction of secondary structure of proteins- Comp
Appli Bioscience 11, 253-260 (1995)
- Casadio R,
Di Bernardo S, Fariselli P, Melandri BA - Characterization of
9-aminoacridine interaction with chromatophore membranes and modelling of
the probe response to artificially induced transmembrane DpH's- Biochim
Biophys Acta 1237, 23-30 (1995)
- Polverini
E, Neyroz P, Fariselli P, Casadio R and Masotti L -The effect of membranes
on the conformation of neuromedin C- Biochim Biophys Res Commun
214:663-668 (1995)
- Compiani
M, Fariselli P, Casadio R - Statistical behaviour of perceptrons: the case
study of the prediction of protein secondary structures- Int J Neur Sys
6:195-199 (Supp 1995)
- Bernardi
F, Bottoni A, Casadio R, Fariselli P and Rigo A - An ab-initio study of
dioxygen binding site of hemocyanin: a comparison between a CASSCF and DFT
approach - Int J Quantum Chem 56:109-116 (1996)
- Fariselli
P and Casadio R -HTP: a neural network based method for predicting the
topology of helical trasmembrane domains in proteins - Comp Appli
Bioscience 12:41-48 (1996)
- Casadio R,
Fariselli P, Taroni C and Compiani M - A predictor of a-helix trasmembrane
domains of proteins based on neural networks- Eur Biophys J
24:165-178 (1996)
- Bernardi
F, Bottoni A, Casadio R, Fariselli P and Rigo A - An ab-initio study of
the mechanism of the binding process of triplet O2 to hemocyanin - Inorg
Chem 35, 5207-5212 (1996)
- Rost B,
Fariselli P, and Casadio R - Topology prediction for helical transmembrane
proteins at 86% accuracy- Protein Science 5, 1704-1718 (1996)
- Compiani
M, Fariselli P, Casadio R - Noise and randomlike behavior of perceptrons:
theory and application to protein structure prediction- Phys Rev E
55, 7334-7343 (1997)
- Vivarelli,
F, Fariselli P and Casadio R - The prediction of protein secondary
structure with a casacade correlation learning architecture of neural
networks- Neural Comput Applic 6, 57-62 (1997)
- Di
Bernardo S, Fato R, Casadio R, Fariselli P, Lenaz G -A high diffusion
coefficient for coenzyme Q10 might be related to a folded structure- FEBS
Lett (1998) 426, 77-80.
- Compiani
M, Fariselli P, Martelli P, Casadio R - An entropy criterion to detect
minimally frustated intermediates in native proteins - Proc Natl Acad
Sci 95, 9290-9294 (1998)
- Arrigo P,
Fariselli P, Casadio R - Can functional regions of proteins be predicted
from their coding sequences? The case study of G-protein coupled receptors
- GENE GC-221:65-110 (1998)
- Compiani
M, Fariselli P, Martelli P, Casadio R - Neural networks to study invariant
features of protein folding- Theor Chem Acc 101:21-26 (1999)
- Fariselli
P, Casadio R - Neural network based predictor of residue contacts in
proteins - Prot Engng 12:15-21 (1999)
- Fariselli
P, Bottoni, A, Bernardi F, Casadio R - Quantum mechanical analysis of
oxygenated and deoxygenated states of hemocyanin: theoretical clues for a
plausible allosteric model of oxygen binding- Protein Science
8:1546-1550 (1999)
- Fariselli
P, Riccobelli P, Casadio R - Role of evolutionary information in
predicting the disulfide-bonding state of cysteine in proteins - Proteins
36:340-346 (1999)
- Casadio R,
Compiani M, Fariselli P, Jacoboni I and Martelli PL - Neural Networks
predict protein folding and structure: artificial intelligence faces
biomolecular complexity. SAR and QSAR in environmental research
11:149-182 (2000)
- Jacoboni
I, Martelli PL, Fariselli P,Compiani M, Casadio R - Predictions of protein
segments with the same amino acid sequence and different secondary
structure: a benchmark for predictive methods. Proteins 41:535-544
(2000)
- Fariselli
P, Casadio R - RCNPRED: a server for the prediction of the residue
co-ordination numbers in proteins- Bioinformatics 17:202-204 (2001)
- Jacoboni
I, Martelli PL, Fariselli P, De Pinto V, Casadio R -prediction of the
transmembrane regions of beta barrel membrane proteins with a neural
network based predictor- Protein sci 10:779-787 (2001)
- Pollastri
G, Baldi P, Fariselli P, Casadio R. -Improved prediction of the number of
residue contacts in proteins by recurrent neural networks- Bioinformatics
Suppl 1:S234-S242 (2001)
- Fariselli
P, Casadio R - Prediction of disulfide connectivity in proteins - Bioinformatics
17:957-964 (2001)
- Fariselli
P, Olmea O, Valencia A, Casadio R - Prediction of contact maps with neural
networks and correlated mutations - Prot Engng 269:835-843 (2001)
- Fariselli
P, Olmea O, Valencia A, Casadio R - Progress in predictiing contact
maps of contact maps of proteins with neural networks and correlated
mutations - Proteins Suppl 5:157-162 (2001)
- Pollastri
G, Baldi P, Fariselli P, Casadio R. -Prediction of coordination number and
relative solvent accessibility in proteins - Proteins
47:142-153 (2002)
- Fariselli
P, Pazos F, Valencia A, Casadio R - Prediction of protein--protein
interaction sites in heterocomplexes with neural networks- Eur J
Biochem 269:1356-1361(2002)
- Martelli
PL, Fariselli P, Krogh A and Casadio R - A Sequence Profile Based HMM for
Predicting and Discriminating Beta Barrel Membrane Proteins - Bioinformatics
18: S46-S53 (2002)
- Casadio R,
Compiani M, Facchiano A, Fariselli P, Martelli PL, Jacoboni I, Rossi I
-Protein structure prediction and biomolecular recognition: from protein
sequence to peptidomimetic design with the human beta 3 integrin- SAR
QSAR Envir Res 13:473-486 (2002)
- Martelli
PL, Fariselli P, Malaguti L, Casadio R. -Prediction of the disulfide
bonding state of cysteines in proteins with hidden neural networks- Protein
Eng. 15:951-953 (2002)
- Rossi I, Marchignoli D, Fariselli P, Beltrami R, Medini D, Casadio R -
DNCBLAST: a parallel BLAST for computer clusters - Minerva
Biotecnologica 15:191-193 (2003)
- Juan D,
Grana O, Pazos F, Fariselli P, Casadio R, Valencia A. -A neural network
approach to evaluate fold recognition results- Proteins 50:600-608
(2003)
- Fariselli
P, Finelli M, Marchignoli D, Martelli PL, Rossi I, and Casadio R
-MaxSubSeq: an algorithm for segment-length optimization. The case study
of the transmembrane spanning segments- Bioinformatics 19:500-505
(2003)
- Casadio R,
Fariselli P, Finocchiaro G, Martelli PL -Fishing new proteins in the
twilight zone of genomes: The test case of outer membrane proteins in
Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative
bacteria- Protein Sci. 6:1158-1168 (2003)
- Martelli
PL, Fariselli P, Casadio R - An ENSEMBLE machine learning approach for the
prediction of all-alpha membrane proteins- Bioinformatics Suppl
1:I205-I211 (2003)
- Martelli
PL, Fariselli P, Tasco G, Casadio R -The prediction of membrane protein
structure and genome structural annotation- Compar Funct Genom 4:406-
409 (2003)
- Fariselli
P, Finocchiaro G, Casadio R -SPEPlip: the detection of signal peptide and
lipoprotein cleavage sites- Bioinformatics 19:2498-2499 (2003)
- Casadio R,
Fariselli P, Martelli PL -In silico prediction of the structure of
membrane proteins: Is it feasible?- Brief Bioinf 4:341-348 (2003)
- Capriotti
E, Fariselli P, Rossi I, Casadio R -A Shannon entropy-based filter detects
high-quality profile-profile alignments in searches for remote homologues
- Proteins 54:351-360 (2004)
- Berezin C,
Glaser F, Rosenberg J, Paz I, Pupko T, Fariselli P, Casadio R, Ben-Tal N
-ConSeq: the identification of functionally and structurally important
residues in protein sequences- Bioinformatics 20:1322-1324 (2004)
- Martelli
PL, Fariselli P, Casadio R -The prediction of disulfide-bonded cysteines
in proteomes with a Hidden Neural Network- Proteomics 4:1665-1671
(2004)
- Capriotti
E, Fariselli P, Casadio R. -A neural-network-based method for predicting
protein stability changes upon single point mutations - Bioinformatics
20 Suppl 1:I63-I68 (2004)
- Capriotti
E, Fariselli P, Casadio R. -I-Mutant2.0: predicting stability changes upon
mutation from the protein sequence or structure- Nucl Acids Res 33:
W306-W310(2005).
- Capriotti
E, Fariselli P, Calabrese R, Casadio R -Predicting protein stability
changes from sequence with Support Vector Machines- Bioinformatics
21:ii54-ii58 (2005).
- Fariselli P, Finelli M, Rossi I, Amico M, Zauli A, Martelli PL,
Casadio R. -TRAMPLE: the transmembrane protein labelling environment- Nucl
Acids Res 33: W198-W201 (2005).
- Fariselli
P, Martelli PL, Casadio R. - A new decoding algorithm for hidden Markov
models improves the prediction of the topology of all-beta membrane
proteins - BMC Bioinformatics 6 Suppl 4:S12 (2005).
- Amico M,
Finelli M, Rossi I, Zauli A, Elofsson A, Viklund H, von Heijne G, Jones D,
Krogh A, Fariselli P, Martelli PL, Casadio R -PONGO: a web server for
multiple predictions of all-alpha transmembrane proteins- Nucleic Acids
Res 34(Web server issue):169-172 (2006)
- Pierleoni A, Martelli PL, Fariselli P, Casadio R - BaCelLo: a balanced
subcellular localization predictor - Bioinformatics 22:e408-e416
(2006)
- Pierleoni A, Martelli PL, Fariselli P, Casadio R - eSLDB: eukaryotic
subcellular localization database - Nucleic Acids Res 35:D208-12
(2007)
- Fariselli
P, Rossi I, Capriotti E, Casadio R - The WWWH of remote homolog detection:
The state of the art.- Brief Bioinform. 8:78-87 (2007)
- Bartoli L,
Calabrese R, Fariselli P, Mita DG, Casadio R - A computational approach
for detecting peptidases and their specific inhibitors at the genome level
- BMC Bioinformatics 8:S3 (2007)
- Tress ML,
Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PL,
Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA,
Lopez G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W,
Storling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramirez F,
Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE,
Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H,
Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A,
Valencia A -The implications of alternative splicing in the ENCODE protein
complement- Proc Natl Acad Sci USA 104:5495-54500 (2007)
- Montanucci
L, Martelli PL, Fariselli P, Casadio R -Robust determinants of
thermostability highlighted by a codon frequency index capable of
discriminating thermophilic from mesophilic genomes- J Proteome Res 6:2502-2508
(2007) (2007)
- Bartoli L., Capriotti E., Fariselli P.,
Martelli P.L., Casadio R. The pros and cons of predicting protein contact
maps- Protein structure prediction. Methods In Molecular Biology 413:199
- 218 (2007)
- Casadio
R.; Fariselli P.; Martelli P.L.; Tasco G. -Thinking the impossible: How to
solve the protein folding problem with and without homologous structures
and more- Methods In Molecular Biology 350:305-320 (2007)
- Bartoli L,
Fariselli P, Casadio R -The effect of backbone on the small-world
properties of protein contact maps- Phys Biol 4:L1-L5 (2008)
- Montanucci
L, Fariselli P, Martelli PL, Rossi I, Casadio R -In Silico Evidence of the
Relationship Between miRNAs and siRNAs- Open Appl Inf Journal
2:9-13 (2008)
- Vassura M,
Margara L, Di Lena P, Medri F, Fariselli P, Casadio R -FT-COMAR: fault
tolerant three-dimensional structure reconstruction from protein contact
maps- Bioinformatics 24:1313-1315 (2008)
- Capriotti
E, Fariselli P, Rossi I, Casadio R -A three-state prediction of single
point mutations on protein stability changes- BMC Bioinformatics 9
Suppl 2:S6 (2008)
- Montanucci
L, Fariselli P, Martelli PL, Casadio R -Predicting protein thermostability
changes from sequence upon multiple mutations- Bioinformatics
24:i190-i195 (2008)
- Vassura M,
Margara L, Di Lena P, Medri F, Fariselli P, Casadio R -Reconstruction of
3D structures from protein contact maps- IEEE/ACM Trans Comput Biol
Bioinform 5:357-367 (2008)
- Vassura M,
Margara L, Fariselli P, Casadio R -A graph theoretic approach to protein
structure selection- Artif Intell Med 45:229-237 (2009)
- Di Lena P,
Vassura M, Margara L, Fariselli P, Casadio R- A On the reconstruction of three-dimensional
protein structures from contact maps- Algorithms. 2(1):76-92
(2009).
- Ezkurdia
I, Bartoli L, Fariselli P, Casadio R, Valencia A, Tress ML -Progress and
challenges in predicting protein-protein interaction sites- Brief
Bioinform 10:233-246 (2009)
- Calabrese
R, Capriotti E, Fariselli P, Martelli PL, Casadio R. - Functional
annotations improve the predictive score of human disease-related
mutations in proteins.- Hum Mutat. 30:1237-1244 (2009).
- Bartoli L,
Montanucci L, Fronza R, Martelli PL, Fariselli P, Carota L, Donvito G,
Maggi G, Casadio R. - The Bologna Annotation Resource: a non-hierarchical
method for the functional and structural annotation of protein sequences
relying on a comparative large-scale genome analysis. J Proteome Res.
8:4362 - 4371 (2009).
- Bartoli
L., Fariselli P., Krogh A., Casadio R. CCHMM_PROF: a HMM-based coiled-coil
predictor with evolutionary information. Bioinformatics.
25:2757-2763. (2009).
- Fariselli
P., Savojardo C., Martelli P.L., Casadio R. Grammatical -Restrained Hidden
Conditional Random Fields for Bioinformatics applications. Algorithms
For Molecular Biology. 22:4 – 13 (2009).
- Fuselli S, de Filippo C, Mona S,
Sistonen J, Fariselli P, Destro-Bisol G, Barbujani G, Bertorelle G,
Sajantila A. - Evolution of DetoxifyingSystems: the Role of Environment
and Population History in Shaping genetic Diversity at Human CYP2D6 Locus-
Pharmacogenetics and Genomics 20:485-99.
(2010)
- Di Lena P,
Fariselli P, Vassura M, Margara L, Casadio R -Fast overlapping of protein
contact maps by alignment of eigenvectors- Bioinformatics 26:2250-2258. (2010)
- Bartoli L,
Martelli PL, Rossi I, Fariselli P, Casadio R -The prediction of
protein-protein interacting sites in genome-wide protein interaction
networks: The Test Case of the Human Cell Cycle- Curr Protein Pept Sci
1;11(7):601-608 (2010).
- Martelli PL, D'Antonio M, Bonizzoni P, Castrignanò T, D'Erchia AM,
D'Onorio De Meo P, Fariselli P, Finelli M, Licciulli F, Mangiulli M,
Mignone F, Pavesi G, Picardi E, Rizzi R, Rossi I, Valletti A, Zauli A,
Zambelli F, Casadio R, Pesole G -ASPicDB: a database of annotated
transcript and protein variants generated by alternative splicing- Nucleic
Acids Res 39:D80-D85 (2011)
- Vassura M,
Di Lena P, Margara L, Mirto M, Aloisio G, Fariselli P, Casadio R - Blurring contact maps of thousands of
proteins: what we can learn by reconstructing 3D structure- BioData Min. 2011 Jan 13;4(1):1.
- Di Lena P,
Fariselli P, Vassura M, Margara L, Casadio R- Is there an optimal
substitution matrix for contact prediction with correlated mutations? IEEE/ACM
Trans. Comput. Biology and Bioinformatics 8(4):1017-1028. (2011).
- Pierleoni
A, Indio V, Savojardo C, Fariselli P, Martelli PL, Casadio R -MemPype: a
pipeline for the annotation of eukaryotic membrane proteins- Nucleic
Acids Res 39:W375-W380 (2011).
- Piovesan
D, Luigi Martelli P, Fariselli P, Zauli A, Rossi I, Casadio R -BAR-PLUS:
the Bologna Annotation Resource Plus for functional and structural
annotation of protein sequences- Nucleic Acids Res 39:W197-W202
(2011).
- Savojardo
C, Fariselli P, Alhamdoosh M, Martelli PL, Pierleoni A, Casadio
R-Improving the prediction of disulfide bonds in Eukaryotes with machine
learning methods and protein subcellular localization- Bioinformatics
27:2224-2230 (2011).
- Casadio R,
Vassura M, Tiwari S, Fariselli P, Martelli PL -Correlating disease related
mutations to their effect on protein stability: a large scale analysis of
the human proteome- Hum Mutat 32:1161-1170 (2011).
- Savojardo
C, Fariselli P, Casadio R -Improving the detection of transmembrane
beta-barrel chains with N-to-1 extreme learning machines- Bioinformatics
27:3123-3128 (2011).
- Juritz E,
Fornasari M, Martelli PL, Fariselli P, Casadio R, Parisi G- On the effect
of protein conformation diversity in discriminating among neutral and disease
related single amino acid substitutions BMC Genomics, 13
(Suppl 4):S5 (2012).
- Martelli
PL, Fariselli P, Balzani E, Casadio R-Predicting cancer-associated
germline variations in proteins- BMC
Genomics, 13 (Suppl 4):S8 (2012).
-
Piovesan D, Martelli PL, Fariselli P, Profiti G, Zauli A, Rossi I, Casadio R -How to inherit statistically validated annotation within BAR+ protein clusters-
BMC Bioinformatics
,
14, Suppl 3:S4 (2013).
-
Savojardo C, Fariselli P, Martelli PL, Casadio R -Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations-
BMC Bioinformatics
,
14, Suppl 1:S10 (2013).
-
Indio V, Martelli PL, Savojardo C, Fariselli P, Casadio -The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields.-
Bioinformatics
,
29:981-988 (2013).
-
Capriotti E, Calabrese R, Fariselli P, Martelli PL, Altman RB, Casadio R.
WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation. -
BMC Genomics.
,
14:S6 (2013).
-
Savojardo C, Fariselli P, Casadio R. BETAWARE: a machine-learning tool to detect and predict transmembrane beta barrel proteins in Prokaryotes -
Bioinformatics
,
29:504-505 (2013).
Protocols and Reports
- Pierleoni
A, Martelli PL, Fariselli P, Casadio R -BaCelLo: a Balanced subCellular
Localization predictor- Nature Protocols DOI:10.1038/nprot.2007.165
(2007)
Referred Proceedings
- Casadio R,
Compiani M, Fariselli P, Vivarelli F -Predicting free energy contribution
to the conformational stability of folded proteins from residue sequence
with radial basis function networks- Proc Conf Intelligent Systems for
Molecular Biology (Rawlings C et al, Eds)Vol 4, pp 81-88, AAAI Press,
California (ismb 1995)
- Compiani
M, Fariselli P, Casadio R- Noise and random-like behaviour of perceptrons:
theory and application to protein structure prediction- In: Application
and Science of Artificial Neural Networks II, (Rogers SK and Ruck DW, Eds.
Proc. Spie 2760) Vol 2760, 587-607
(1996)
- Arrigo P,
Fariselli P, Casadio R - The identification of locally ordered features on
completely unligned genomic sequences by using an unsupervised neural
classifiers- In: Computer Science and Biology, Proc of the German
conference on Bioinformatics (GBC '96) (Hofestadt R et al., eds) pp
156-159, Leipzig 1996
- Rost B,
Casadio R, Fariselli P - Refining neural network predictions for helical
transmembrane proteins by dynamic programming - In : Proc. Fourth
International Conference on Intelligent Systems for Molecular Biology
(States DJ et al, Eds) Vol 4, pp 192-200, AAAI Press, California (ismb
1996)
- Fariselli
P, Casadio R (1997)- Pseudodihedral potential of protein residues and the
prediction of folding- In: Proc Bio-Computing and Emergent Computation
BCEC 97 (1997) (Lundth D et al, eds), pp112-121,World Scientific,
Singapore
- Arrigo P,
Fariselli P, Casadio R (1997) - Self-organizing neural map of the coding
sequences of G-Protein- coupled receptors reveal local domains associated
with potentially functional determinants in the proteins- In : Proc Fifth
International Conference on Intelligent Systems for Molecular Biology
(Gaasterland T et al, eds) Vol 5, pp44-47, AAAI Press, California (ismb
1997)
- Fariselli
P, Casadio R (1998)- A neural network based method for predicting contact
maps of proteins -Proc. of World Multiconference on Systemics, Cybernetics
and Informatics (SCI'98, Orlando USA) Vol 1, pp 527-533
- Casadio R,
Arrigo P,Fariselli P, (1998)- Self-organizing neural networks highlight
possible functionally relevant regions in the c-DNA coding sequences of
G-protein coupled receptors - Proc. of the First international conference
on bioinformatics of genome regulation and structure (BGRS'98,
Novosibirisk 1998) Vol 2, pp 262-265
- Casadio R,
Compiani M, Fariselli P, Martelli PL (1999) - A data base of minimally
frustrated alpha helical segments extracted from proteins according to an
entropy criterion- In : Proc Seventh International Conference on
Intelligent Systems for Molecular Biology (Lengauer et al, eds) Vol 7,
pp68-76, AAAI Press, California (ismb 1999)
- Fariselli
P, Casadio R - Prediction of the Number of Residue Contacts in
Proteins- ISMB 7: 146-151 (2000) (ismb 2000)
- Fariselli
P, Martelli P, Casadio R - A neural network based method for predicting
the disulfide connectivity in proteins- Knowledge based intelligent
information engineering systems and allied technologies (KES 2002),
(Damiani E et al., eds), Vol 1, pp 464-468, IOS Press, Amsterdam
(2002)
- Rossi I,
Marchignoli D, Medini D, Beltrami R, Donati C, Fariselli P, Covacci A,
Casadio R -A simple yet effective implementation of a parallel BLAST for
computer clusters- Proc. Virt. Conf. Genom. and Bioinf. 1 (2002)
11-16
- Fariselli
P, Zauli A, Rossi I, Finelli M, Martelli PL, Casadio R - A neural network
method to improve prediction of protein-protein interaction sites in
heterocomplexes- IEEE International Workshop on Neural Network on Signal
Processing 2003 Toulouse (FRANCE) IEEE Press 33-41 (2003)
- Fariselli
P, Finocchiaro G, and Casadio R - Prediction of Signal Peptide in Proteins
with Neural Networks - Lecture Notes in Computer Science (2003)
2859 237 – 244
- Fariselli
P, Molinini D, Casadio R, Krogh A - Prediction of Structurally-Determined
Coiled-Coil Domains with Hidden Markov Models- Lect Notes Comp Sci 4414:292-302
(2007)
- Mirto M,
Rossi I, Epicoco I, Fiore S, Fariselli P,Casadio R, Aloisio G -High
throughput protein similarity searches in the LIBI Grid problem solving
environment- Lect Notes Comp Sci 4743:414-423 (2007)
- Vassura M,
Margara L, Di Lena P, Medri F, Fariselli P, Casadio R -Fault tolerance for
large scale protein 3D reconstruction from contact maps- Lect Notes
Comp Sci 4645:25-37 (2007)
- Vassura M,
Margara L, Fariselli P, Casadio R -A graph theoretic approach to protein
structure selection- Lect Notes Comp Sci 4578:497-504 (2007)
- Vassura M,
Margara L, Medri F, Di Lena P, Fariselli P, Casadio R -Reconstruction of
3D structures form protein contact maps- Lect Notes Comp Sci
4463:578-589 (2007)
- Carota L,
Bartoli L, Fariselli P, Martelli PL, Montanucci L, Maggi G, Casadio R -
High Throughput Comparison of Prokaryotic Genomes- Lect Notes Comp Sci
4967:1200-1209 (2008)
- Di Lena P,
Fariselli P, Vassura M, Margara L, Fariselli P, Casadio R - On the upper
bound of the prediction accuracy of residue contacts in proteins with
correlated mutations: the case study of the similarity matrices- Proc. of the 9th International
Workshop on Algorithms in Bioinformatics (WABI2009), Pennsylvania
(2009)
108.
Bartoli L, Fariselli P, Bartoli L, -
PS-COILS: a new method for coiled-coil prediction that exploits both
single-sequence and evolutionary information- Procedings of the sixth
international meeting on Computational Intelligence methods for Bioinformatics
and Biostatistics (CIBB09), vol. 3, pp. 1 – 8 (2009).
- Bartoli
L., Martelli P.L., Rossi I., Fariselli P., Casadio R. Prediction of
Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large
Scale Protein Interaction Networks. Lect Notes Comp Sci. vol.
5688:1 - 17 (2009).
- Fariselli
P, Bartoli L, Casadio R- Improving coiled-coil prediction with
evolutionary information- Lect Notes Comp Sci. 6160:20-32 (2010).
- Savojardo
C, Fariselli P, Martelli PL, Shukla P, Casadio R. Prediction of cysteine bonding state with
machine-learning methods. Procedings of the sixth
international meeting on Computational Intelligence methods for
Bioinformatics and Biostatistics (CIBB10) Vol. 4. (2010).
Others
- Compiani
M, Fariselli P, Casadio R- Neural Networks extracting general features of
protein secondary structures-In: Parallel Architectures and Neural
Networks (Caianiello ER, ed) pp 227-237, World Scientific, Singapore
(1991)
- Compiani
M, Fariselli P, Casadio R- The statistical behaviour of perceptrons-In:
Parallel Architectures and Neural Networks (Caianiello ER, ed) pp 111-117,
World Scientific, Singapore (1992)
- Compiani
M, Fariselli P, Casadio R - Neural networks and prediction of protein
structures - In"Neural Networks in Biology and Medicine", pp
313-332, World Scientific, Singapore (1994)
- Fariselli
P, Taroni C, Compiani M, Casadio R - Application of neural networks to the
prediction of protein structures-In: Primo Seminario di Bioinformatica
(Colosimo A, ed), pp 257-274, CNR and University of Camerino (1994)
- Fariselli
P, Hubbard T, Ortigao FR and Reinhardt A - Crococage: a protein
designed to bind cholesterol - In EMBO Protein Design Course '95
(Vriend G and Sander S , ed) (1995)
- Casadio R,
Fariselli P, Rigo A -The role of ligands on the mechanism of oxygen
binding to hemocyanin: an ab-initio study based on the density functional
theory- Science and Supercomputing at CINECA (1995)
118. Papa M, Campanini R, Fariselli P, Casadio R, Erbacci G, Vivarelli F,
Giusti G -Prediction of protein secondary structures using a committeee of
neural networks- Science and Supercomputing at CINECA (1995)
119. Martelli PL, Fariselli P, and Casadio R - De novo design of
proteins: the alpha-helix enginner- In: Italian Biochemical Society
Transactions (IBST) Vol. 8, 38-39 (1997) (Invited Speaker at Proteine '97)
120. Fariselli P, Casadio R (1998)- A neural Network based method for
predicting contact maps of proteins Simai '98, Vol 1, pp 272-275
121. Casadio R, Fariselli P, Rigo A -Computational analysis of oxygenated
and deoxygenated states of hemocyanin: theoretical support for a putative
allosteric model of oxygen binding - Science and Supercomputing at CINECA
(1998)
122. Fariselli P, Casadio R - Quantum molecular biophysics: the case
study of hemocyanin- in Biophysics of Electron Transfer and Molecular
Bioelectronics (Nicolini C, ed) E.L:B.A. Forum Series Vol.3, pp 139-159, Plenum
Pub Co, New York (1998)
123. Rossi E, Boschi S, Cozzini S, Casadio R, Rossi I, Fariselli P,
Arnofi E, Riccobelli P, Facchiano A (1999) -Protein modeling combining Homology
Building and Molecular Dynamics- ECCC5 (http://hackberry.chem.niu.edu/ECC5)
124. Casadio R, Rossi I, Fariselli P, Arnofi E, Ricobelli P, Rossi E,
Boschi S, Facchiano A-DRUG- Supercomputing Drug design for Industrial and
Academic Partnership. Peptidomimetic molecules active on vascular cell growth
and migration- In HPCN Experiences in Biotechnology (Dechema and GMD eds) pp
1-25, Frankufurt (1999)
125. Casadio R, Compiani M, Fariselli P, Jacoboni I, Martelli PL, Rossi I
-Tools for protein secondary structure prediction: from sequence to structure-
In "Protein sequence analysis in the Post Genomic Era" (Casadio E and
Masotti L eds) 115-133, CLUEB, Bologna (2001)
126. Casadio R, Fariselli P -From protein sequence to structure with
Neural Networks- In: Protein Folding, Stability and Design 2002, (Gromiha MM
and Selvaraj S, eds.) pp 79-92, Research Signpost Editions, Trivandrum, India
(2002)
127. Piero Fariselli, Michele Finelli, Davide Marchignoli, Rita Casadio
"MaxSubSeq:an algorithm for finding all the maximal scoring subsequences
with costrained segment lengths" AIIA, VIII Convegno (Siena, 10-13/9/2002)
a cura di Gori M. pp. 12-12, AI*IA, Siena, 2002
128. Casadio R, Capriotti E, Compiani M, Fariselli P, Jacoboni I,
Martelli PL, Rossi I, Tasco G -Neural Networks and the prediction of protein
structure. In Artificial Intelligence and Heuristic Methods in Bioinformatics.
(Frasconi P and Shamir R, eds) pp. 22-33. NATO Science Series. IOS Press,
Amsterdam,Netherlands, (2003)