Barbara Di Camillo

Barbara Di Camillo

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Barbara Di Camillo

Barbara Di Camillo

Publications by authors named "Barbara Di Camillo"

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Diabetes diagnosis from administrative claims and estimation of the true prevalence of diabetes among 4.2 million individuals of the Veneto region (North East Italy).

Nutr Metab Cardiovasc Dis 2020 Jan 9;30(1):84-91. Epub 2019 Sep 9.

Department of Medicine, University of Padova, Padova, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.numecd.2019.08.017DOI Listing
January 2020

metaSPARSim: a 16S rRNA gene sequencing count data simulator.

BMC Bioinformatics 2019 Nov 22;20(Suppl 9):416. Epub 2019 Nov 22.

Department of Information Engineering, University of Padova, via Giovanni Gradenigo, 6, Padova, 35131, Italy.

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http://dx.doi.org/10.1186/s12859-019-2882-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6873395PMC
November 2019

SPARSim Single Cell: a count data simulator for scRNA-seq data.

Bioinformatics 2019 Oct 9. Epub 2019 Oct 9.

Department of Information Engineering, University of Padova, Padova, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btz752DOI Listing
October 2019

A Dynamic Bayesian Network model for the simulation of Amyotrophic Lateral Sclerosis progression.

BMC Bioinformatics 2019 Apr 18;20(Suppl 4):118. Epub 2019 Apr 18.

Department of Information Engineering, University of Padova, Gradenigo 6/b, 35131, Padova, Italy.

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http://dx.doi.org/10.1186/s12859-019-2692-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6471677PMC
April 2019

Measuring the diversity of the human microbiota with targeted next-generation sequencing.

Brief Bioinform 2018 07;19(4):679-692

Department of Information Engineering, University of Padova, Padova, Italy.

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http://dx.doi.org/10.1093/bib/bbw119DOI Listing
July 2018

HAPT2D: high accuracy of prediction of T2D with a model combining basic and advanced data depending on availability.

Eur J Endocrinol 2018 Apr 25;178(4):331-341. Epub 2018 Jan 25.

EndocrinologyAbdominal Centre, University of Helsinki and Helsinki University Hospital, Research Program for Diabetes and Obesity, University of Helsinki, Helsinki, Finland

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http://dx.doi.org/10.1530/EJE-17-0921DOI Listing
April 2018

Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods.

Front Genet 2017 23;8:62. Epub 2017 May 23.

Department of Information Engineering, University of PadovaPadova, Italy.

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http://dx.doi.org/10.3389/fgene.2017.00062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5440469PMC
May 2017

bnstruct: an R package for Bayesian Network structure learning in the presence of missing data.

Bioinformatics 2017 04;33(8):1250-1252

Department of Information Engineering, University of Padova, 35131 Padova, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btw807DOI Listing
April 2017

Simulation-based comprehensive benchmarking of RNA-seq aligners.

Nat Methods 2017 02 12;14(2):135-139. Epub 2016 Dec 12.

Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1038/nmeth.4106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5792058PMC
February 2017

A rule-based model of insulin signalling pathway.

BMC Syst Biol 2016 06 1;10(1):38. Epub 2016 Jun 1.

Department of Information Engineering, University of Padova, Via Gradenigo 6A, Padova, 35131, Italy.

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http://dx.doi.org/10.1186/s12918-016-0281-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4888568PMC
June 2016

A Dynamic Bayesian Network model for long-term simulation of clinical complications in type 1 diabetes.

J Biomed Inform 2015 Oct 29;57:369-76. Epub 2015 Aug 29.

Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Italy.

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http://dx.doi.org/10.1016/j.jbi.2015.08.021DOI Listing
October 2015

Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis.

Brief Funct Genomics 2015 Mar 18;14(2):130-42. Epub 2014 Sep 18.

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http://dx.doi.org/10.1093/bfgp/elu035DOI Listing
March 2015

Toxicogenomic markers for corticosteroid treatment in beef cattle: integrated analysis of transcriptomic data.

Food Chem Toxicol 2015 Mar 19;77:1-11. Epub 2014 Dec 19.

Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, 35020 Legnaro, Padova, Italy.

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http://dx.doi.org/10.1016/j.fct.2014.12.001DOI Listing
March 2015

Early origins of adult disease: low birth weight and vascular remodeling.

Atherosclerosis 2014 Dec 30;237(2):391-9. Epub 2014 Sep 30.

Department of Woman and Child Health, University of Padua School of Medicine, Padua, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.atherosclerosis.2014.09.027DOI Listing
December 2014

Compression and fast retrieval of SNP data.

Bioinformatics 2014 Nov 26;30(21):3078-85. Epub 2014 Jul 26.

Department of Information Engineering, University of Padova, via Gradenigo 6/a, 35131 Padova, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btu495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609015PMC
November 2014

SimBioNeT: a simulator of biological network topology.

IEEE/ACM Trans Comput Biol Bioinform 2012 18;9(2):592-600. Epub 2011 Aug 18.

University of Padova, Padova.

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http://ieeexplore.ieee.org/document/5999655/
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http://dx.doi.org/10.1109/TCBB.2011.116DOI Listing
May 2014

ABACUS: an entropy-based cumulative bivariate statistic robust to rare variants and different direction of genotype effect.

Bioinformatics 2014 Feb 28;30(3):384-91. Epub 2013 Nov 28.

Department of Information Engineering, University of Padova, via Gradenigo 6B, 35131 Padova, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btt697DOI Listing
February 2014

Retrovirus HTLV-1 gene circuit: a potential oscillator for eukaryotes.

Pac Symp Biocomput 2010 :421-32

Department of Information Engineering, University of Padua, via Gradenigo 6, Padua 35131, Italy.

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November 2013

Bag of Naïve Bayes: biomarker selection and classification from genome-wide SNP data.

BMC Bioinformatics 2012 7;13 Suppl 14:S2. Epub 2012 Sep 7.

Department of Information Engineering, University of Padova, 35131 Padova, Italy.

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http://dx.doi.org/10.1186/1471-2105-13-S14-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439675PMC
May 2013

A large-scale evaluation of computational protein function prediction.

Authors:
Predrag Radivojac Wyatt T Clark Tal Ronnen Oron Alexandra M Schnoes Tobias Wittkop Artem Sokolov Kiley Graim Christopher Funk Karin Verspoor Asa Ben-Hur Gaurav Pandey Jeffrey M Yunes Ameet S Talwalkar Susanna Repo Michael L Souza Damiano Piovesan Rita Casadio Zheng Wang Jianlin Cheng Hai Fang Julian Gough Patrik Koskinen Petri Törönen Jussi Nokso-Koivisto Liisa Holm Domenico Cozzetto Daniel W A Buchan Kevin Bryson David T Jones Bhakti Limaye Harshal Inamdar Avik Datta Sunitha K Manjari Rajendra Joshi Meghana Chitale Daisuke Kihara Andreas M Lisewski Serkan Erdin Eric Venner Olivier Lichtarge Robert Rentzsch Haixuan Yang Alfonso E Romero Prajwal Bhat Alberto Paccanaro Tobias Hamp Rebecca Kaßner Stefan Seemayer Esmeralda Vicedo Christian Schaefer Dominik Achten Florian Auer Ariane Boehm Tatjana Braun Maximilian Hecht Mark Heron Peter Hönigschmid Thomas A Hopf Stefanie Kaufmann Michael Kiening Denis Krompass Cedric Landerer Yannick Mahlich Manfred Roos Jari Björne Tapio Salakoski Andrew Wong Hagit Shatkay Fanny Gatzmann Ingolf Sommer Mark N Wass Michael J E Sternberg Nives Škunca Fran Supek Matko Bošnjak Panče Panov Sašo Džeroski Tomislav Šmuc Yiannis A I Kourmpetis Aalt D J van Dijk Cajo J F ter Braak Yuanpeng Zhou Qingtian Gong Xinran Dong Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Barbara Di Camillo Stefano Toppo Liang Lan Nemanja Djuric Yuhong Guo Slobodan Vucetic Amos Bairoch Michal Linial Patricia C Babbitt Steven E Brenner Christine Orengo Burkhard Rost Sean D Mooney Iddo Friedberg

Nat Methods 2013 Mar 27;10(3):221-7. Epub 2013 Jan 27.

School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA.

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http://dx.doi.org/10.1038/nmeth.2340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584181PMC
March 2013

Qualitative reasoning for biological network inference from systematic perturbation experiments.

IEEE/ACM Trans Comput Biol Bioinform 2012 Sep-Oct;9(5):1482-91

Department of Information Engineering, University of Padova, Padova, Italy.

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http://dx.doi.org/10.1109/TCBB.2012.69DOI Listing
January 2013

MORE: mixed optimization for reverse engineering--an application to modeling biological networks response via sparse systems of nonlinear differential equations.

IEEE/ACM Trans Comput Biol Bioinform 2012 Sep-Oct;9(5):1459-71

Department of Information Engineering, University of Padova, Padova, Italy.

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http://dx.doi.org/10.1109/TCBB.2012.56DOI Listing
January 2013

Confined 3D microenvironment regulates early differentiation in human pluripotent stem cells.

Biotechnol Bioeng 2012 Dec 20;109(12):3119-32. Epub 2012 Jun 20.

Department of Industrial Engineering (DII), University of Padua, via Marzolo 9, 35131 Padua, Italy.

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http://dx.doi.org/10.1002/bit.24571DOI Listing
December 2012

Integrating literature-constrained and data-driven inference of signalling networks.

Bioinformatics 2012 Sep 25;28(18):2311-7. Epub 2012 Jun 25.

Department of Information Engineering, University of Padova, Padova, 31050, Italy.

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http://dx.doi.org/10.1093/bioinformatics/bts363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436796PMC
September 2012

Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data.

Brief Bioinform 2012 May 21;13(3):269-80. Epub 2011 Oct 21.

Information Engineering Department of the University of Padova, Padova, Italy.

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http://dx.doi.org/10.1093/bib/bbr063DOI Listing
May 2012

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.

BMC Bioinformatics 2012 Mar 28;13 Suppl 4:S14. Epub 2012 Mar 28.

Department of Molecular Medicine, University of Padova, via U. Bassi 58/B, 35121, Padova, Italy.

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http://dx.doi.org/10.1186/1471-2105-13-S4-S14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3314586PMC
March 2012

Improving biomarker list stability by integration of biological knowledge in the learning process.

BMC Bioinformatics 2012 Mar 28;13 Suppl 4:S22. Epub 2012 Mar 28.

Department of Information Engineering, University of Padova, via G, Gradenigo 6/B, 35131 Padova, Italy.

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http://dx.doi.org/10.1186/1471-2105-13-S4-S22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3314566PMC
March 2012

Dynamic modeling of miRNA-mediated feed-forward loops.

J Comput Biol 2012 Feb;19(2):188-99

Department of Information Engineering, University of Padova, Padova, Italy.

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http://dx.doi.org/10.1089/cmb.2011.0274DOI Listing
February 2012

Hemodynamics assessed via approximate entropy analysis of impedance cardiography time series: effect of metabolic syndrome.

Am J Physiol Heart Circ Physiol 2011 Aug 13;301(2):H592-8. Epub 2011 May 13.

Department of Information Engineering, University of Padova, Padova, Italy.

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http://dx.doi.org/10.1152/ajpheart.01195.2010DOI Listing
August 2011

Sensitivity analysis of retrovirus HTLV-1 transactivation.

J Comput Biol 2011 Feb;18(2):183-93

Department of Information Engineering, University of Padova, Padova, Italy.

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http://www.liebertpub.com/doi/10.1089/cmb.2010.0219
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http://dx.doi.org/10.1089/cmb.2010.0219DOI Listing
February 2011

Draft genome sequences of two Neisseria meningitidis serogroup C clinical isolates.

J Bacteriol 2010 Oct 30;192(19):5270-1. Epub 2010 Jul 30.

Department of Histology, Microbiology, and Medical Biotechnologies, University of Padua, Via A. Gabelli, 63-35121 Padua, Italy.

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http://dx.doi.org/10.1128/JB.00789-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944513PMC
October 2010

A Boolean approach to linear prediction for signaling network modeling.

PLoS One 2010 Sep 16;5(9). Epub 2010 Sep 16.

Department of Information Engineering, University of Padova, Padova, Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012789PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940821PMC
September 2010

An optimized data structure for high-throughput 3D proteomics data: mzRTree.

J Proteomics 2010 Apr 16;73(6):1176-82. Epub 2010 Feb 16.

Department of Information Engineering, University of Padova, Padova Italy.

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http://dx.doi.org/10.1016/j.jprot.2010.02.006DOI Listing
April 2010

A gene network simulator to assess reverse engineering algorithms.

Ann N Y Acad Sci 2009 Mar;1158:125-42

Information Engineering Department, University of Padova, Padova, Italy.

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http://dx.doi.org/10.1111/j.1749-6632.2008.03756.xDOI Listing
March 2009

Significance analysis of microarray transcript levels in time series experiments.

BMC Bioinformatics 2007 Mar 8;8 Suppl 1:S10. Epub 2007 Mar 8.

Information Engineering Department, University of Padova, 35131 Padova, Italy.

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http://dx.doi.org/10.1186/1471-2105-8-S1-S10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885839PMC
March 2007

Use of a novel triple-tracer approach to assess postprandial glucose metabolism.

Am J Physiol Endocrinol Metab 2003 Jan;284(1):E55-69

Division of Endocrinology, Diabetes, Metabolism, and Nutrition, Department of Internal Medicine, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA.

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http://www.physiology.org/doi/10.1152/ajpendo.00190.2001
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http://dx.doi.org/10.1152/ajpendo.00190.2001DOI Listing
January 2003