Publications by authors named "Federico M Giorgi"

45Publications

coronapp: A Web Application to Annotate and Monitor SARS-CoV-2 Mutations.

J Med Virol 2020 Nov 18. Epub 2020 Nov 18.

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

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http://dx.doi.org/10.1002/jmv.26678DOI Listing
November 2020

Web tools to fight pandemics: the COVID-19 experience.

Brief Bioinform 2020 Oct 15. Epub 2020 Oct 15.

University of Bologna.

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http://dx.doi.org/10.1093/bib/bbaa261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7665357PMC
October 2020

Svpluscnv: analysis and visualization of complex structural variation data.

Bioinformatics 2020 Oct 14. Epub 2020 Oct 14.

Genetics and Genomics Sciences, Icahn School of Medicine, New York, USA.

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http://dx.doi.org/10.1093/bioinformatics/btaa878DOI Listing
October 2020

Predicting the response of the dental pulp to SARS-CoV2 infection: a transcriptome-wide effect cross-analysis.

Genes Immun 2020 11 3;21(5):360-363. Epub 2020 Oct 3.

Department of Endodontics, School of Dentistry, University of Texas Health and Sciences Center, San Antonio, TX, 78229, USA.

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http://dx.doi.org/10.1038/s41435-020-00112-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7532735PMC
November 2020

Differential submergence tolerance between juvenile and adult Arabidopsis plants involves the ANAC017 transcription factor.

Plant J 2020 Nov 28;104(4):979-994. Epub 2020 Sep 28.

Plantlab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.

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http://dx.doi.org/10.1111/tpj.14975DOI Listing
November 2020

Geographic and Genomic Distribution of SARS-CoV-2 Mutations.

Front Microbiol 2020 22;11:1800. Epub 2020 Jul 22.

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

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http://dx.doi.org/10.3389/fmicb.2020.01800DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7387429PMC
July 2020

Transcriptional network inference and master regulator analysis of the response to ribosome-inactivating proteins in leukemia cells.

Toxicology 2020 08 25;441:152531. Epub 2020 Jun 25.

Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.tox.2020.152531DOI Listing
August 2020

Spathial: an R package for the evolutionary analysis of biological data.

Bioinformatics 2020 Nov;36(17):4664-4667

Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genoa 16163, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btaa273DOI Listing
November 2020

Master Regulator Analysis of the SARS-CoV-2/Human Interactome.

J Clin Med 2020 Apr 1;9(4). Epub 2020 Apr 1.

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

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http://dx.doi.org/10.3390/jcm9040982DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7230814PMC
April 2020

corto: a lightweight R package for gene network inference and master regulator analysis.

Bioinformatics 2020 Jun;36(12):3916-3917

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

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http://dx.doi.org/10.1093/bioinformatics/btaa223DOI Listing
June 2020

Gene network reverse engineering: The Next Generation.

Biochim Biophys Acta Gene Regul Mech 2020 06 5;1863(6):194523. Epub 2020 Mar 5.

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http://dx.doi.org/10.1016/j.bbagrm.2020.194523DOI Listing
June 2020

Genomic variance of the 2019-nCoV coronavirus.

J Med Virol 2020 05 19;92(5):522-528. Epub 2020 Feb 19.

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

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http://dx.doi.org/10.1002/jmv.25700DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166773PMC
May 2020

Gene regulatory network inference resources: A practical overview.

Biochim Biophys Acta Gene Regul Mech 2020 06 31;1863(6):194430. Epub 2019 Oct 31.

Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.bbagrm.2019.194430DOI Listing
June 2020

Pan-Cancer and Single-Cell Modeling of Genomic Alterations Through Gene Expression.

Front Genet 2019 18;10:671. Epub 2019 Jul 18.

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

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http://dx.doi.org/10.3389/fgene.2019.00671DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6657420PMC
July 2019

A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.

Cell Stem Cell 2018 04;22(4):575-588.e7

Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.03.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957284PMC
April 2018

Age-dependent regulation of ERF-VII transcription factor activity in Arabidopsis thaliana.

Plant Cell Environ 2017 Oct 30;40(10):2333-2346. Epub 2017 Aug 30.

Scuola Superiore Sant'Anna, Institute of Life Sciences, Plantlab, Via Guidiccioni 8/10, 56017, Pisa, Italy.

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http://dx.doi.org/10.1111/pce.13037DOI Listing
October 2017

Functional characterization of somatic mutations in cancer using network-based inference of protein activity.

Nat Genet 2016 08 20;48(8):838-47. Epub 2016 Jun 20.

Department of Systems Biology, Columbia University, New York, New York, USA.

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http://dx.doi.org/10.1038/ng.3593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5040167PMC
August 2016

Detection and removal of spatial bias in multiwell assays.

Bioinformatics 2016 07 28;32(13):1959-65. Epub 2016 Feb 28.

Department of Biomedical Informatics (DBMI) Department of Systems Biology Center for Computational Biology and Bioinformatics (C2B2), Columbia University, New York, NY, USA Department of Biochemistry and Molecular Biophysics Institute for Cancer Genetics Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw092DOI Listing
July 2016

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.

Bioinformatics 2016 07 23;32(14):2233-5. Epub 2016 Apr 23.

Department of Systems Biology, Columbia University, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937200PMC
July 2016

Inferring protein modulation from gene expression data using conditional mutual information.

PLoS One 2014 14;9(10):e109569. Epub 2014 Oct 14.

Department of Systems Biology, Columbia University, New York, New York, United States of America; Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109569PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196905PMC
June 2015

CEBPA-regulated lncRNAs, new players in the study of acute myeloid leukemia.

J Hematol Oncol 2014 Sep 25;7:69. Epub 2014 Sep 25.

Department of Biology and Biotechnology C, Darwin, Sapienza University of Rome, Rome, 00185, Italy.

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http://dx.doi.org/10.1186/s13045-014-0069-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177583PMC
September 2014

An extensive evaluation of read trimming effects on Illumina NGS data analysis.

PLoS One 2013 23;8(12):e85024. Epub 2013 Dec 23.

Institute of Applied Genomics, Udine, Italy ; Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0085024PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3871669PMC
October 2014

Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana.

Bioinformatics 2013 Mar 1;29(6):717-24. Epub 2013 Feb 1.

Institute of Applied Genomics, Udine 33100, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btt053DOI Listing
March 2013

LASSO modeling of the Arabidopsis thaliana seed/seedling transcriptome: a model case for detection of novel mucilage and pectin metabolism genes.

Mol Biosyst 2012 Oct;8(10):2566-74

Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.

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http://dx.doi.org/10.1039/c2mb25096aDOI Listing
October 2012

Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization.

Nature 2011 Oct 23;479(7373):419-22. Epub 2011 Oct 23.

Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany.

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http://dx.doi.org/10.1038/nature10536DOI Listing
October 2011

Algorithm-driven artifacts in median polish summarization of microarray data.

BMC Bioinformatics 2010 Nov 11;11:553. Epub 2010 Nov 11.

Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Golm, Germany.

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http://dx.doi.org/10.1186/1471-2105-11-553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998528PMC
November 2010

Structural analysis of the RZZ complex reveals common ancestry with multisubunit vesicle tethering machinery.

Structure 2010 May;18(5):616-26

Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, I-20139 Milan, Italy.

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http://dx.doi.org/10.1016/j.str.2010.02.014DOI Listing
May 2010

Transcriptional wiring of cell wall-related genes in Arabidopsis.

Mol Plant 2009 Sep 30;2(5):1015-24. Epub 2009 Jul 30.

Max-Planck-Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany.

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http://dx.doi.org/10.1093/mp/ssp055DOI Listing
September 2009

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats.

Plant Cell Environ 2009 Dec 27;32(12):1633-51. Epub 2009 Aug 27.

Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.

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http://doi.wiley.com/10.1111/j.1365-3040.2009.02040.x
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http://dx.doi.org/10.1111/j.1365-3040.2009.02040.xDOI Listing
December 2009

Low duplicability and network fragility of cancer genes.

Trends Genet 2008 Sep 31;24(9):427-30. Epub 2008 Jul 31.

Department of Experimental Oncology, European Institute of Oncology, Milan, Italy.

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http://dx.doi.org/10.1016/j.tig.2008.06.003DOI Listing
September 2008