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List of works by Federico Manuel Giorgi

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

scientific article published in April 2018

A modular master regulator landscape controls cancer transcriptional identity

scientific article published on 11 January 2021

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

scientific article

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

scientific article published on 25 July 2017

Algorithm-driven artifacts in median polish summarization of microarray data

scientific article

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

scientific article

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

scientific article

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

scientific article published on 27 August 2009

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

scientific article

Correction to: VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer

scientific article published on 14 June 2019

Correction: Inferring Protein Modulation from Gene Expression Data Using Conditional Mutual Information

scientific article published on 15 September 2016

Corticosteroid sensitization drives opioid addiction

scholarly article

DNA Repair Biomarker for Lung Cancer Risk and its Correlation With Airway Cells Gene Expression

scientific article published on 12 September 2019

Detection and removal of spatial bias in multiwell assays

scientific article

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

scientific article published on 29 August 2020

Escalated (Dependent) Oxycodone Self-Administration Is Associated with Cognitive Impairment and Transcriptional Evidence of Neurodegeneration in Human Immunodeficiency Virus (HIV) Transgenic Rats

scientific article published on 24 March 2022

Exploiting the molecular basis of age and gender differences in outcomes of SARS-CoV-2 infections

scientific article published on 10 July 2021

Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon

scientific article published on 15 June 2017

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

scientific article published on 20 June 2016

Gene network reverse engineering: The Next Generation

scientific article published on 05 March 2020

Gene regulatory network inference resources: A practical overview

scientific article published on 31 October 2019

Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera

scientific article

Genomic variance of the 2019-nCoV coronavirus

scientific article

Genomic variance of the 2019-nCoV coronavirus

scientific article published on 19 February 2020

Geographic and Genomic Distribution of SARS-CoV-2 Mutations

scientific article published on 22 July 2020

High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing.

scientific article

Histone Deacetylases (HDACs): Evolution, Specificity, Role in Transcriptional Complexes, and Pharmacological Actionability

scientific article published on 15 May 2020

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

scientific article

Inhibition of polyamine synthesis and uptake reduces tumor progression and prolongs survival in mouse models of neuroblastoma

scientific article published on 01 January 2019

Intra-tumoral copper modulates PD-L1 expression and influences tumor immune evasion

scientific article published on 18 August 2020

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

scientific article published in October 2012

Low duplicability and network fragility of cancer genes

scientific article published on 31 July 2008

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

scientific article published on 01 April 2020

Master Regulator Analysis of the SARS-CoV-2/Human interactome

scientific article (preprint)

Misexpression of a chloroplast aspartyl protease leads to severe growth defects and alters carbohydrate metabolism in Arabidopsis

scientific article published on 17 September 2012

Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses

scientific article published on 14 September 2020

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

scientific article published on 23 October 2011

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

scientific article published on 18 July 2019

PlaNet: combined sequence and expression comparisons across plant networks derived from seven species

scientific article published on 25 March 2011

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

scientific article published on 03 October 2020

Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K

publication published on 15 May 2021

Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis

scientific article

SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data

scientific article

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

scientific article

Structural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex

scientific article published on 13 February 2021

Svpluscnv: analysis and visualization of complex structural variation data

scientific article published on 14 October 2020

The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability

scientific article (publication date: September 2013)

The R Language: An Engine for Bioinformatics and Data Science

publication published on 27 April 2022

The Transcriptome of SH-SY5Y at Single-Cell Resolution: A CITE-Seq Data Analysis Workflow

scientific article published in 2021

Transcriptional Network Inference and Master Regulator Analysis of the Response to Ribosome-Inactivating Proteins in Leukemia Cells

scientific article published on 25 June 2020

Transcriptional Wiring of Cell Wall-Related Genes in Arabidopsis

article

Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum).

scientific article

VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer

scientific article published on 13 May 2019

VULCAN: Network Analysis of ER-α activation reveals reprogramming of GRHL2

Wage rigidities and business cycle fluctuations: a linked employer-employee analysis

article published in 2016

Web tools to fight pandemics: the COVID-19 experience

scientific article published on 15 October 2020

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

scientific article published on 18 November 2020

corto: a lightweight R package for Gene Network Inference and Master Regulator Analysis

scientific article published on 31 March 2020

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