Castrense Savojardo

Castrense Savojardo

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Castrense Savojardo

Castrense Savojardo

Publications by authors named "Castrense Savojardo"

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Assessing predictions on fitness effects of missense variants in calmodulin.

Hum Mutat 2019 Jul 8. Epub 2019 Jul 8.

Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas, 75390-9050, USA.

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http://dx.doi.org/10.1002/humu.23857DOI Listing
July 2019

Assessing predictions of the impact of variants on splicing in CAGI5.

Hum Mutat 2019 Jul 13. Epub 2019 Jul 13.

Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.

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http://dx.doi.org/10.1002/humu.23869DOI Listing
July 2019

DeepMito: accurate prediction of protein submitochondrial localization using convolutional neural networks.

Bioinformatics 2019 Jun 20. Epub 2019 Jun 20.

Biocomputing Group, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btz512DOI Listing
June 2019

Are machine learning based methods suited to address complex biological problems? Lessons from CAGI-5 challenges.

Hum Mutat 2019 May 8. Epub 2019 May 8.

Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.

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http://dx.doi.org/10.1002/humu.23784DOI Listing
May 2019

Functional and Structural Features of Disease-Related Protein Variants.

Int J Mol Sci 2019 Mar 27;20(7). Epub 2019 Mar 27.

Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.

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https://www.mdpi.com/1422-0067/20/7/1530
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http://dx.doi.org/10.3390/ijms20071530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6479756PMC
March 2019

Draft genomes and genomic divergence of two Lepidurus tadpole shrimp species (Crustacea, Branchiopoda, Notostraca).

Mol Ecol Resour 2019 Jan 19;19(1):235-244. Epub 2018 Oct 19.

Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.

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http://doi.wiley.com/10.1111/1755-0998.12952
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http://dx.doi.org/10.1111/1755-0998.12952DOI Listing
January 2019

On the biases in predictions of protein stability changes upon variations: the INPS test case.

Bioinformatics 2018 Nov 29. Epub 2018 Nov 29.

Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (Padova), Italy.

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http://dx.doi.org/10.1093/bioinformatics/bty979DOI Listing
November 2018

BUSCA: an integrative web server to predict subcellular localization of proteins.

Nucleic Acids Res 2018 07;46(W1):W459-W466

Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40100, Italy.

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https://academic.oup.com/nar/article/46/W1/W459/4990035
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http://dx.doi.org/10.1093/nar/gky320DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031068PMC
July 2018

DeepSig: deep learning improves signal peptide detection in proteins.

Bioinformatics 2018 05;34(10):1690-1696

Biocomputing Group, Department of Pharmacy and Biotechnology - Interdepartmental Centre 'L. Galvani' for Integrated Studies of Bioinformatics, Biophysics and Biocomplexity, University of Bologna, 40126 Bologna, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btx818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5946842PMC
May 2018

eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes.

BMC Genomics 2017 08 11;18(Suppl 5):554. Epub 2017 Aug 11.

Biocomputing Group, BiGeA, University of Bologna, Bologna, Italy.

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http://dx.doi.org/10.1186/s12864-017-3911-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5558190PMC
August 2017

ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model.

Bioinformatics 2017 Jun;33(11):1656-1663

Biocomputing Group, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btx044DOI Listing
June 2017

SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments.

Bioinformatics 2017 02;33(3):347-353

Biocomputing Group, BiGeA - CIG, Interdepartmental Center «Luigi Galvani» for Integrated Studies of Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btw656DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408801PMC
February 2017

INPS-MD: a web server to predict stability of protein variants from sequence and structure.

Bioinformatics 2016 08 10;32(16):2542-4. Epub 2016 Apr 10.

Biocomputing Group, CIG, Interdepartmental Center «Luigi Galvani» for Integrated Studies of Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Italy Interdepartmental Center «Giorgio Prodi» for Cancer Research, University of Bologna, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btw192DOI Listing
August 2016

Large scale analysis of protein stability in OMIM disease related human protein variants.

BMC Genomics 2016 06 23;17 Suppl 2:397. Epub 2016 Jun 23.

Biocomputing Group, University of Bologna, Via San Giacomo 9/2, 40126, Bologna, Italy.

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http://dx.doi.org/10.1186/s12864-016-2726-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928156PMC
June 2016

Computer-based prediction of mitochondria-targeting peptides.

Methods Mol Biol 2015 ;1264:305-20

Biocomputing Group, CIRI Health Sciences & Technologies (HST), University of Bologna, Bologna, Italy.

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http://link.springer.com/10.1007/978-1-4939-2257-4_27
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http://dx.doi.org/10.1007/978-1-4939-2257-4_27DOI Listing
October 2015

TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins.

Bioinformatics 2015 Oct 16;31(20):3269-75. Epub 2015 Jun 16.

Biocomputing Group, University of Bologna, Department of Biology, 40126 Bologna, Italy and.

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http://dx.doi.org/10.1093/bioinformatics/btv367DOI Listing
October 2015

INPS: predicting the impact of non-synonymous variations on protein stability from sequence.

Bioinformatics 2015 Sep 7;31(17):2816-21. Epub 2015 May 7.

Biocomputing Group, Department of Biology, University of Bologna, 40126 Bologna and.

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http://dx.doi.org/10.1093/bioinformatics/btv291DOI Listing
September 2015

TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs.

Bioinformatics 2014 Oct 27;30(20):2973-4. Epub 2014 Jun 27.

Biocomputing Group, University of Bologna, CIRI-Health Science and Technology/Department of Biology, 40126 Bologna and Department of Computer Science and Engineering, University of Bologna, 40127 Bologna, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btu411DOI Listing
October 2014

BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming.

Bioinformatics 2013 Dec 23;29(24):3151-7. Epub 2013 Sep 23.

Biocomputing Group, CIRI-Health Science and Technology/Department of Biology, University of Bologna, 40126 Bologna, Italy and Department of Computer Science and Engineering, Via Mura Anteo Zamboni 7, 40127 Bologna, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btt555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5994943PMC
December 2013

Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations.

BMC Bioinformatics 2013 14;14 Suppl 1:S10. Epub 2013 Jan 14.

Department of Computer Science and Engineering, University of Bologna, Via Mura Anteo Zamboni 7, 41029 Bologna, Italy.

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http://dx.doi.org/10.1186/1471-2105-14-S1-S10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548674PMC
August 2013

The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields.

Bioinformatics 2013 Apr 21;29(8):981-8. Epub 2013 Feb 21.

Biocomputing Group, and Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna, Bologna, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btt089DOI Listing
April 2013

BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes.

Bioinformatics 2013 Feb 6;29(4):504-5. Epub 2013 Jan 6.

Biocomputing Group, CIRI-Health Science and Technology/Department of Biology, University of Bologna, 40126 Bologna, Italy.

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http://dx.doi.org/10.1093/bioinformatics/bts728DOI Listing
February 2013

Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines.

Bioinformatics 2011 Nov 3;27(22):3123-8. Epub 2011 Oct 3.

Biocomputing Group, Department of Biology, University of Bologna CIRI-Health Science and Technology, 40126 Bologna, Italy.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btr549DOI Listing
November 2011

Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization.

Bioinformatics 2011 Aug 29;27(16):2224-30. Epub 2011 Jun 29.

Biocomputing Group, University of Bologna, CIRI-Life Science and Health Technologies and Department of Biology, Via San Giacomo 9/2, Bologna, Italy.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btr387DOI Listing
August 2011

MemPype: a pipeline for the annotation of eukaryotic membrane proteins.

Nucleic Acids Res 2011 Jul 4;39(Web Server issue):W375-80. Epub 2011 May 4.

Externautics s.p.a.-Bioinformatics, Via Fiorentina 1, 53100 Siena, Italy.

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http://dx.doi.org/10.1093/nar/gkr282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125734PMC
July 2011

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications.

Algorithms Mol Biol 2009 Oct 22;4:13. Epub 2009 Oct 22.

Biocomputing Group, University of Bologna, via Irnerio 42, 40126 Bologna, Italy.

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http://almob.biomedcentral.com/articles/10.1186/1748-7188-4-
Publisher Site
http://dx.doi.org/10.1186/1748-7188-4-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776008PMC
October 2009